Here's what people need to understand - and largely don't seem to, for some strange reason given how straightforward and self-explanatory the whole thing is - about the new Star Trek films: they are effectively an 'AU' that was created by catastrophic events in the universe that spawned TOS and its movies, TNG and its movies, DS9, VOY, and ENT and really do not in any way constitute a relevant example with regards to what may or may not be happening with the X-Men franchise going forward insofar as timelines and chronology are concerned.
The closest analogue I can think of for what appears to be happening with the X-Men franchise is Nintendo's The Legend of Zelda franchise and its multi-tiered chronology as outlined in the Hyrule Historia reference book.