I don't remember where I read it, but I remember someone telling me there are individual rights holders for specific Final Fantasy tracks, but SQEX can kind of override that when it's their product but not when it isn't (so like why they can make stuff like Theatrhythm). It goes beyond just Uematsu apparently.People keep bringing up music rights being all over the place for Final Fantasy, but unlike Dragon Quest where the music has Sugiyama listed as the copyright holder, Square Enix themselves are always listed as the copyright holder for Final Fantasy music (and indeed other franchises like SaGa). Granted, I haven't looked at absolutely every case but I doubt we'd be getting stuff like Florence and the Machine's FFXV tracks anyway.
The only person/party I can think of that is listed as a separate copyright holder for anything Final Fantasy is Amano for the logo designs. I guess the same would be true for Amano's other artworks for the series but they are often more abstract takes on the character designs.
I'll post it if I can find the source of that.