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I hex-edited the Ground Zeroes idle face animation sna0face_idl_lp.gani into something The Phantom Pain can read, and replaced TPP's equivalent with that conversion. It's pretty much the most different animation, being much more detailed and bigger than the rest, so I didn't bother converting more of them.
It takes a lot of fiddling and knowing how the format works to do this, so unfortunately, no, there's no custom animation tools yet, but hopefully this proof of concept shows that we know what the format does enough to manually convert these between game versions. I used the 010 Editor template here to help with the hex-editing, and it helped a lot.