With the caveat that I don't know enough about Blender to double check any of this, I saw an interesting twitter post that may explain why a lot of these differences are happening.
https://i.imgur.com/HXCyLTv.png
https://i.imgur.com/sQTfWxa.png
https://i.imgur.com/ado5aym.png
This tracks with what I've observed about the new models. I don't think they've actually been 100% redone (though I think some of the mouth differences might be touch ups, and there's definitely new teeth in there, plus the previously mentioned 50 new bones). But they've been put through the Blender equivalent of a belt sander. It smooths out the polygons, but without additional detail work some of the character of the original sculpt gets lost.
The differences in the lips in the examples above is pretty stark once you're looking at it without any lighting or texture. The definition of the cupid's bow is much less visible because of the smoothing. Same thing with the shape and size of the nose/nostrils.
I've also noticed that the bugs that the original face meshes had (neck gaps, face seams) still seem to be there, to a greater or lesser extent.