I have this exact same problem when importing a mesh as a Reference Mesh. It's imported and placed as a Paint Object which the Smart Retopo tool doesn't seem to like. To make it work I had to go to the Paint Room and go to Bake > Paint Mesh->Sculpt Mesh. That turned it into a Surface under the SculptTree. Smart Retopo tool seems to work way better when it is a Sculpt object.
I kind of get why 3DCoat has all this stuff separate, but it would be way less confusing if all the different types of objects were not there. We don't really need a Paint Object, Sculpt Object, Poly Groups, whatever else for geometry. Geometry is geometry. Blender for example has one geometry object that you can sculpt on, poly model with, UV, use for retopo, and paint on without conversions needed. It's simple. We don't need 3 different groups for geometry. There is a little letter next to the geometry for Sculpt (S) and Voxel (V) maybe add a Low Poly (L), but also let the sculpt be used for painting and making UVs without conversion needed. Instead to get it ready for paint have a warning that says "This geometry has no UVs" if it doesn't have UVs. Baking high poly to low poly should be an option available between any 2 geometries. Just a "Bake high to low" tool that pops up saying "Pick high geom" "Pick low geom". It doesn't need to be so complex with all these conversions. Going even another step further Sculpt and Voxel doesn't even need to be there as a hybrid could be used where if a sculpt tool is used it moves and changes the points under the brush like if it were a sculpt object and Voxel could change the points under only the brush area like if it was Voxel.