Here's Simon Kinberg's explanation"[X-Men: Apocalypse] takes space chronologically before those other films, so it’s more like those films have to acknowledge this than we acknowledge Gambit, Deadpool, or Fantastic Four or anything else that exists within the sort of Fox/Marvel universe. But I work on all of those films in one capacity or another, either as a producer on all of them and as a writer on Fantastic Four and this movie, so I’m certainly aware of all the different stories we’re telling at the same time, and they all are part of a larger fabric now, and so the world of Deadpool, the world of Gambit exists in a post-Days of Future Past post-Apocalypse world where all of these stories are the same as our shared history. The same way that each of us of different ages knows about Nixon and knows about Reagan and knows about 9/11, our fictitious events like the stadium dropping on the White House in 1973 is part of the world in which Gambit, Deadpool, Wolverine on forward exists."
Bryan Singer adds, "I rebooted the universe so now anything can happen," with the caveat that their theory of time-travel and alternate universes revolve around immutability, in that things may differ, but key events in every timeline will remain mostly similar. Xavier will always form the X-Men, Wolverine will always enlist in Weapon X and get his adamantium claws, and Wade Wilson will always become a version of Deadpool.