specifically, can I set the deformer to affect only certain polygons? I've looked for this option and can't find it if it exists.
No, sadly. There was some discussion of this, for a DFOrtm Pro plugin perhaps, way back but nothing came of it. It would be very useful with the way the mesh is a single item now - please feel free to make a feature request.
Darn... need to create a morph and this will make it doubly difficult :(