Logan is not set in the established X-Men Universe. Any of them.
In an interview with Digital Spy, Logan star Hugh Jackman reveals that the newest and presumably last time he dons the claws takes place in a "slightly different universe".
"When you see the full movie you'll understand,"
"Not only is it different in terms of timeline and tone, it's a slightly different universe. It's actually a different paradigm and that will become clear."
"It's a stand alone movie in many ways."
"It's not really beholden to time lines and story lines in the other movies. Obviously Patrick Stewart was in there so we have some crossover but it feels very different and very fresh."
In all fairness, as anyone who has read Old Man Logan can attest, that run comic takes place in an alternate future, so this news is surprising/not surprising.
Hugh goes on to discuss the overall tone of the movie and how it's not really a Wolverine movie, but more of a movie about an old guy who has to come to terms with being Wolverine his whole life.
"I said this was my last one and they said make the movie you want to make,"
"And so Jim [Mangold] and I had this blank canvas and we wanted to make something really different. Definitely tonally different, I kept thinking The Wrestler, Unforgiven.
"He was thinking Unforgiven as well and The Gauntlet and these other movies which just seemed to really match his character. Early on we had the idea for the title not having anything to do with Wolverine in it but just being about the man. And what the collateral damage of being Wolverine your entire life would be."
All in all, I don't really have a problem with any of this. I come at these movies from the view of a lifelong comic book fan, so an alternate universe arc doesn't frighten me. I'm sure the same goes for a lot of people who will see this movie. It's the non-comic book reading movie goers that might find this a bit overwhelming.
Come to think of it, I've got a few concerns now too. Does this mean we won't be seeing X-23 in one of the proper X-Men universes? If we do, will she have a totally new origin story? How will the forthcoming "soft reboot" of the X-Men universe affect X-23 and other characters from the Wolverine movies that don't "count"? How about Deadpool? How do he and his X-Force universe fit in?
Maybe Logan takes place in the F Universe. FU for short? Whatever universe it's called, it's not going to stop me from seeing Logan on or around March 3, 2017.