Except Fox doesn't own the theme park rights to X-Men, Marvel does, and Universal is the only theme park operator to hold onto the Marvel rights. It's the reason why Fox has to get permission from Disney/Marvel to co-produce Legion and the Gifted for the FX or Fox networks.
Marvel as the owner of all of its properties has a final say over the Marvel products used at IOA's MSHI, not Fox. After all, as you said, Fox owns the X-Men as a licensee as a film right, not as a 100% owner, so Universal has to get permission from Marvel to use characters from the X-Men movies instead. The fact is, the 1994 contract clearly states Universal can make any ride based off whatever property they want and the only permission they need to make changes/add Marvel attractions is from Marvel itself, not Fox.