digman

No substance type of material export like in Substance Designer from 3DC. You will need to export your 3DC maps to Substance Designer...

Geometry Menu
Define Measurement Units. I set mine to meters as I do not need to be precise as you do... I have not messed about with the other settings in the panel.
Edit Scene Scale...  The bottom line is the only one you need to worry about... default is 1.00, which as you know is huge. I set it to 100..00 to match Blender's metric scale. Blender's two meter cube imports into 3DC at that real world scale. I do not know what you would need to in 3DC's scale to match other software. 
 
Study the measure tool's panel closely... You can snap your cuts to the measuring line, set your measure units without having to go to the Geometry menu and adjust the main scene measurement units. etc...
Note: "Show in other tools" If the measure tool lines disappear when selecting another tool, create an empty layer, click on that layer, then click back to the original layer and the lines will appear. Appears to be a disappearing bug.
Note: Hold down the shift key to have a straight line.
Note: Even if you scale an object when importing, the Measurement units remain the same. a meter cube will still be a meter cube if you scale it up for voxel mode density.
 To create a base scene-----Close 3DC and reopen to a new empty scene set your scale and measure units. Now save that scene as your base 3DC scene.
 
Hope the above helps some...

In Surface mode... Top menus---Freeze menu----Hide Frozen.

The below is the most used way of what you are asking for. I am assuming you are in the 3DC sculpt room as you used the word "Layer".
 
Watch these videos. Start at video 14 which cover autopo and the next 2 manual retopo. 
Keep watching the rest of the videos oh how to bake to the paint room for your normal map and painting your textures.
 
This series is for the beginner and does not cover all situations... I do not know how your model is laid out or whether you have any object occluding layers. 
The second video will cover how to handle that situation.
 

I think what you meant by Palette is really Panel, at least that is what I am assuming by your description.
 
Windows menu----Popups---Tool Presets.
 
Netural Zone borders
Camera---Customize Navigation---Scroll to the bottom of the panel
Deselect the first box... put the other two at "0'

The below might or might not help. I do not have a picture of your 3DC interface.
 
Adding the below information just to be on the safe side.
 
Did you scale along one axis when using the transform tool. Do you have a red warning at the bottom of 3DC's interface that reads "Non Uniform"
 
If so, right click on the model and look in the panel till you see "To Global Space", Select it and it will fixed the distorted voxels. 
Voxels are 3D cube pixels and just like a 2D image, if you stretch them in a non-aspect ratio fashion you will distort them just like you would 2D pixels.
Once the voxels are fixed you will have a easier time fixing any areas that need it. 
 
A Tip... just another workflow...
 
Instead of using the transform tool to stretch the object, first select the cube primitive. Then transform to the proper dimensions you need for the object you be will be creating. Press enter or apply to create the real mesh.
 
Ortho mode.
You will be doing an inverse boolean operation. 
Use the close spline or load shape and the cut off tool to create your shape.
Now hold down the Shift + Ctrl keys. Left click with mouse or tablet pen.
The material will be cut off on outside of the close spline leaving your shape with no transforming needed. 

Here is a quick video I did today on the basic workflow... The quality is not the best and no editing is done but it is clear enough.
The video does not include all the various ways and hows of doing the workflow but only shows the most basic functions on a simple rock object.
Once you understand that, then learning in more detail comes easier.
I will make better videos in the future but these are done quickly to answer a user's specific questions.
Once through the workflow, of course ask any other questions that arise.
 
For your information: The low polygon mesh I imported was a decimate mesh to 4000 polygons of the the high polygon mesh. That is a similar method that was used in the Unreal Engine 4 Kite demo for rocks...
For some reason in the video, I said Unreal 3. go figure...   
In the video, I chose to import without voxelization which imports a model into surface polygon mode. Scaling with the gizmo does not increase the polygon count.
If your model is all quads it will triangulate the model only,
 
You can import into voxel mode but might need to scale up the object to get the require voxel density to capture all the details.
 

1.000 is full opacity..
1.000 is full depth
Both can manually be set past 1.000
 
If you are using a tablet and pen, the clone tool is still sensitive to pen pressure. 
Choose the brush type shown in the attached image so the brush pen is no longer sensitive to pressure.
 
A Tip:
If you need the brush radius to be sensitive to pen pressure and still need opacity at 100%, set the opacity value somewhere around 10.0 to 20.0 in the tool's panel. I just use 20.0 and I have a perfect match, though 10 should be ok, maybe less that.. I have not tested.
This works good for the first brush type from the e-panel.

Layer Tool... Vox Layer?
 
Possible solution if you meant the back faces of the object or in other words the opposite side of the object. 
Check the E-Panel and make sure "Ignore Back Faces" is enabled. When using a spline tool in the E-panel this needs to be enabled.
 
Can you make a video of the problem if this does not fix it or I misunderstood what tool you were using.

When working with 3DC PBR materials everything from setting up in 3DC and Max needs to be done correctly. I do not have Max but know online others who do and have seen the applink in action.
 
Install the new completely rewritten 3DCoat --- Max plugin... AbnRanger is I believe going make a new video for the new plug-in rewrite. He has Max..
Presets I know it has is are IRay and Mental Ray and others but not for Vray atm. You can create one for VRay.
http://3dcoat.com/forum/index.php?showtopic=18802
 
Setup your workflow to use the Gloss / Color Specular  workflow, Located under the Textures window.
Choose a shader to work with. Under the View menu... Which one works best, I do not know maybe AbnRanger can tell you. Test otherwise.
 
The new applink will do nearly all your work for you in creating the materials to be rendered.
 
Here is a video made before the complete rewrite. I believe now that your 3DC materials will be auto imported and attached through the node system. All overwrites of gamma will be setup as well per material. This video will give you at least how the basic functions of the applink work..
 
AbnRanger, might drop in here as well with more complete information. Of course all setting up of materials for rendering can be done by hand without the help of the applink but knowing what and how to setup is the key.  
https://www.youtube.com/watch?v=Pwde7LiJA38

First problem with the star alpha could have been related to this problem the user had in another thread. You had selected the Strips star alpha.
http://3dcoat.com/forum/index.php?showtopic=18775
 
The pressure indicator, not sure what is happening there. The only thing I know to do for now is check under the brush options panel, check the "Depth Modulator".
If it is a minus number your pressure indicator inside the yellow ring will be inverted.

Look at the attached image...
right click on the voxtree tab----go to import--- select point cloud
 
You mentioned that it was a point cloud and not a point cloud that as been generated into a 3D model has of yet if I am not mistaken. I have never tried to import a point cloud to let you know. 

I think it might be related to this bug with the drag stamp or the regular stamp spline from the e-panel. I noticed in your image that the drag stamp tool is selected.
 
I can use the voxel extrude brush with either of the above splines then click undo and the mesh gets corrupted. 
 
I have mentioned this in the beta thread but that can be overlooked. Will post a bug report soon.
 
The bug is still preset in beta version 4.5.27 

1: Create a folder to place your alphas in, your choice of location on your hard drive.
2. Create your alphas in Photoshop or another paint program. Save the alphas to your created folder. This acts as storage folder.
3:Open 3DC, go to the alpha panel and select the Folder icon with the + symbol, create your folder and name it.
4. Select New in the folder, then open texture file.  Not only can you open a texture file but an obj model as well to be used as an alpha.
5. Select your alpha.
6. Your alpha is stored internally in the Textures / Patterns folder of 3DC that is under your User name in windows.
Done and now you have your user created alpha folder, which also can be shared as a extension.
 
2 images attached to this post.
 
The video though old is still the way it works... I will share for others to view.
 

What version of 3DC are you using. Professional--- Educational.
Where in detail are you trying to export from?
What does your export image file formats look like for your color (diffuse) file.
I have attached an image of mine... File Menu \  Export Objects and Textures.
 
Second image is from
Textures Menu
Export Color / Albedo 
 
3rd image 
Textures menu 
Import Color / Albedo
 
 

Your import panel just appears to be squeezed into a smalller space in the panel. Use your mouse cursor to enlarge the panel both horizontally and vertically some.
You mentioned that you wanted instances, I selected it and when you select Instances, import as child is no longer presented as an import option. As you know 3DC is tool selection sensitive.
Also when you select "On Brush" the Yaw, Jitter Yaw, Pitch etc (top of panel)... and shift xyz appear (bottom of panel). You have not selected it in your attached image.
The negative number, I seen that a few times but can not remember clearly why it happen. Whether it is a bug or not, I do not have enough information as of yet to make a educated guess. 

My answer was for the sculpt room.
 
A little tired today, first thing I should have asked is "which room you imported your model into" I had assumed you were in the sculpt room with an object you had imported but sculpted on and now desired to render...
Transforming in the retopo room is only for your retopo mesh, not the sculpt model or imported model into the paint room. 
To transform an object in the paint room, you must switch to the Tweak room. The gizmo works different there and has no input by degrees. 
 
It would be as easy to change the axis direction in another 3D modeling package as well.
 
Old video 9 ( 4 years) for rotating models that were imported into the paint room but it shows you how it is done and still applies. Sculpt next to Paint was change to Tweak.
Go to 1:13 in the video to see how.
 
We have been asking the 3DC developers to make the Tweak Room transform tool to be the same as the rest of the interface. 
 
Hopefully this gets you what you need... LOL and I answered again without knowing for sure how you imported your model...
 

It could be that you have selected that alpha in the Strips Tool panel.  
 
When using the strips tool it locks the brush alpha to the strip selected alpha.
Your other regular alpha is blended with the strip alpha but it favors the strip alpha.
Click on close in the panel to disable the strips tool.
 
Strip tool common workflow is selecting a standard circular alpha and then select your Strips tool alpha.
Example: Creating zippers on a jacket.

Sorry for misunderstanding and yes I did understand that you were not trying to select a tab etc but the line painting part I failed to understand.
You can zoom the texture editor uv area in and out by holding down the right mouse button to prevent you from going over to other areas of 3DC Coat. If you need more texture editor room, move the texture editor to the main 3DC interface and enlarge it. 
I fill very cramp when it is docked myself, like painting on a small piece of paper though not everyone feels that cramped feeling as I do.
 
I setup a hotkey for the Texture Editor. It also can be access under the Textures menu as well.
 
Hope the above helps some.

There is no mesh in the UV room till you bake to the Paint Room.  
Once you create your seams and an unwrap in the retopo room, you are ready to bake or export the model with the uv set.
The name of the uv set is shown in the attached image and if you need to create more uv sets plus renaming.
Also if you have an external model that needs it's uv set adjusted, the uv room is good for that.
 
After baking if you need to adjust the uv set, go to the uv room adjust and then apply that uv set to the paintroom without re-baking. There are a few things to know when doing this concerning the normal map but I will explain when we get together. Plus I can go over about creating new uv sets, moving islands between them etc. etc...
 
At the top of the 3DC forum website is a link to Mantis for bug reporting. There was an issue with not being able register at mantis but you will need to check to to see if it is still occurring,

It can be a little tricky at times moving layers to a group but after a little practice you get the hang of it.
First click on the layer.
Make sure your cursor is in this location, shown in attached image.
When moving the layer, I found that putting the layer name just a tiny bit below the group name that it goes into the group nearly all the time. That seems to be the sweet spot for dropping the layer into a group. 

This method worked on my side.
3DC version 4.5.25. GL--non--cuda--64 bit. Whether you have to choose GL over DX I did not test.
 
View menu
Select-- Compatibility Shader
 
Texture menu
Select--Texture export / import workflow-- Gloss/Color Specular
 
Png was exported with transparency. I opened the image in Photoshop. The transparency was there. 
I did not test in Unity but I know the transparency is in the png file so it should work.
 
The metal/roughness workflow with the GGX shader did not work... Since this did not work, I changed to the above settings. I did not test any other settings methods as this one worked out ok.
 
Attached image shows the png file in Photoshop with the checkerboard transparency background.

This made be your problem. 
Under the View menu, go down the list till you see "Show Voxels in Paint Room", deselect it...
The voxel / surface mode model will always appear in the paint room in case you desire to polypaint (vertex paint) without using a uv set.
Use the View menu to hide it or hide the model under the voxtree tab / Layer eye icon.

The Autopo routine still needs fine tuning, in my opinion, then it will be a more friendly and useful tool.
 
Here are the basic pointers.
Autopo in Voxel mode. The reason why is too much of a chance in surface mode to have hidden holes and mesh intersections as you are dealing with polygons in surface mode. 
These will cause the autopo routine just to crash 3DC, keep running or take a very longggggggggggg time to finish and the result is not good also.
Run Fill Voids (Voxtree tab) to remove any hidden holes in the mesh before running the autopo routine.
Clone the object and run smooth all a few times, to get rid of detail noise. This is covered in the first video. Once you get a clean retopo mesh, hide the cloned object or delete it and now bake to the paint room using the highest detail object.
Less quide strokes are better.
 
I could add more but posting video links instead.
 
Older video on Auto-retopo for organic but still good information. The autopo routine has been updated since then and the panel has changed.
Also there there are two on hard surface as well.
 
If possible share one of your meshes that you are having troubles with and let others see if they can get a good result and report back here to you.
 

Thanks for the picture it helps.
You have your 3 separate retopo meshes on the same "Retopo Objects" Layer. Add a Retopo Objects layer for your skin, shirt and jacket.
Also you can hide (eye icon) the parts of the model and retopo layers you are not working on and only work on one layer at a time.
 
Retopo Objects layer panel is next to the Vox Tree panel. Since you have all the polygons on the same layer it will be a little work to select and move the polygons to the new layers. Examine the icons at the bottom of the retopo objects layer and have your tool tips on to read each function.
 
If you desired only one retopo mesh and not separate retopo meshes for each part of the model, then read below.
Import the model into Voxel mode not surface mode has you have done and do not select "Import has child"
Increase the resoluton enough to capture all the details of the model. The model will be combined as one voxel object.
Now you can retopo using only one Retopo Objects Layer if you so desire. 
 
Side note: I do not know how the model is constructed with the separate parts so importing as one voxel object could cause some problems but that is beyond the scope of this post atm as I do not have enough information to advise on possible problems or solutions.
 
If possible you can always share the model for others to test...