I haven't tried your scripts, so I don't know if it's happening or not, but based on my understanding of what you're doing, even a perfect line-up of the meshes might still have this problem, depending on the topology and shaping of the mesh in some areas.

If you "correlate the (up to) 5 closest verts, within some tolerance distance", one or more of those closest verts could be on the other side of a mesh fold.

If the check adds much time, you could always make it an option.

EDIT: Of course... depending on how some morph is created, this may not be an issue anyway (ie. the morph creator may have also included those vertices within the morph) - so you may not always 'see' that there's a problem.  The only time it might show up is on something like a morph that made the nostril opening smaller/larger diameter, without affecting the outside of the nostril.

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