If I understand what you're saying, I think a variant of your #2 procedure is currently in use.  Right now I'm 'mapping' vertices in one mesh to vertices in another, then transferring adjusted morph deltas between them.  I don't really compare the meshes beyond finding the verts to correlate with one another, and I don't look at the 'shape' of the mesh beyond normalizing and applying the morph deltas.  I think Ockham's NoPoke uses something more like procedure #1, in which he compares the world vertex positions and moves the verts of one mesh to adapt to the shape of the other.  Hmm.  I've been thinking more interms of the difference between vertex and surface comparisons or between comparing the base geometry and the world vertex geometry.  I'll have to think about what you're saying.

Once the vertex mapping is in place, it seems like it could be used as a point of reference for matching two meshes's default shapes.  Earlier I speculated about using the mapping to try to adjust one object's UV's to line them up with another object's.  This at least seems feasible, but I do have a tendency to assume things will be simpler than they turn out to be.  :-P

The trick will be getting the mapping down effectively.  I'm not sure whether the 'raycasting' method of looking for line-plane intersections will return better correlations than the current method, which just tries to find the closest vertex.  Presumably they'll both have similar limitations and somewhat different strengths and weaknesses....  It would be hard to get uglier than some of the results I've ended up with while experimenting with the current vertex method.  Hoo boy.

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Cage can be an opinionated jerk who posts without thinking.  He apologizes for this.  He's honestly not trying to be a turkeyhead.

Cage had some freebies, compatible with Poser 11 and below.  His Python scripts were saved at archive.org, along with the rest of the Morphography site, where they were hosted.