Not only GF environments I think. For example I have a pretty high suspect that Squall's blasting zone animation includes 3d geometry as well as Quezacotl's entry animation. That is based on the moving clouds which looks moving like the battle stage clouds, in circular rotation.
Yep!
I don't know how many .X file reference you found.. but since they have the same extension of battle stages I guessed that they could be the "environment" that sometimes game show during certain animations..it could make sense..
There could be many other file format in the exe (we already know it contains many .tim texture).
There should be many magic that clearly use 3D geometry (for example all the ice ones) but in most of case we have "somehow animated mesh" that we usually don't find elsewhere.
Another thing that has not been considered yet could be bone scaling.
I remember I read once here or on xentax that bone scaling is not used in this game but that's actually not entirely true..
I can think to only a sample of bone scaling but I'm actually sure it's used for GF Pandemona "tail" inflating animation..
Moreover there is Bomb/Piros "enraging animation".. even if that animation is not a bone scaling animation..more probably is scripted..
Many of magic geometry animation anyway could (probably) use bone scaling and I think we should keep that in mind