Actually, you already have this workflow...if you are working with a Paint Mesh in Microvertex mode. Single Mesh, but different layers can store different blendshapes, such as phonemes and visemes. I asked Andrew to enable this when using PPP mode, but I don't think he has gotten around to it. Sometimes we have to ask him more than once, because he is often right in the middle of a big feature request. In this case, a new brush engine is on tap.
The workflow above is not a huge problem because most Blendshapes/Morph Targets have separate copies of a head mesh with the different expressions, but a Morph modifier is used to drive one mesh with all those different meshes hidden in the outliner panel.
So, you could use a base retopo mesh > save it to the RETOPO MODELS pallet and click on that base mesh thumbnail each time you are ready to create a new morph target/blendshape. When you are all done creating the various Blendshapes, using Sculpt Layers for the High Poly sculpt and different Retopo meshes, for the low poly, you can unhide all the new low poly blendshape/morph target meshes in the Retopo Room > go to the RETOPO menu EXPORT. It should export all visible meshes. In an app like Maya or 3ds Max, you just import those in and pick them in your Blendshapes/Morph Target modifier.