Hi,
SlicerSALT was mentioned in a previous thread ("Averaging" 3D models) but I don’t have personal experience with it.
For a research project previously, I’ve used the GIAS2 package in Python to build a statistical shape model from a number of mandibles. One of the components of the shape model is an average structure. The only caveat is that I do not know if it will work with only 2 samples.