I'm inclined to agree.
The X-Universe has always been its own thing, even in the comics. Especially since the 1990s, X-Men has spawned a ****-ton of titles that exist in their own mutant universe. Shlock like the recent AVX notwithstanding, the X-Universe rarely intrudes on the rest of the Marvel Universe, and vice versa. That's why having a separate studio manage the X-Men titles doesn't feel forced at all, and is actually canonical when you think about it.
But yeah, trying to carve out a niche in the X-Universe for the FF *does* feel forced. It's understandable why Fox wants to do it, but it's really apples and oranges. Tonally and thematically, the FF share a lot more with the MCU than with the FCU. Fox, and fandom, would be better served by expanding the X-Men universe by spinning off films like Cable and/or Deadpool, Excalibur, New Mutants, Generation X, X-Factor, X-Statix, The Brotherhood, Storm, Psylocke, Dazzler, Cloak and Dagger....pretty much an infinite bunch of stories to draw from.