Cage:

Far be it from me to be a Blender advocate. The best thing that one can say about Blender is that it is free. It was worth a few hours of research though.

Thanks for explaining the problems with Shrinkwrap. I understand more of the issues involved now. As I read the limited documentation, Retopo will allow you to choose just the vertices you want to project onto your target figure. It must be from a lined up point of view. If you can undo mistakes, then by trial and error, you could eventually accomplish what you want. It would probably be a very arduous process, requiring that you hide about everything you do not want to affect on the target, and the object being Retopo-ed. You would need to do that about every time you took another step. Ouch. If you had to do this for each figure you might want to compare, then $595 (USD) for ZBrush begins to sound cheap.

Seeing that Blender uses Python for scripting. You might have better luck writing your own comparison utility in Blender.

Maybe someone else will have another application to suggest..

LMK

Probably edited for spelling, grammer, punctuation, or typos.