I know that James Mangold has said that it takes place 5 years after the end of DOFP (when Logan wakes up in the mansion) but I’ve always viewed Logan as being standalone & existing in a “possible” future, as sort of Dark Knight Returns scenario. So Wolverine being alive in a Deadpool movie (which have never been overly faithful to the continuity of the X-films anyway) doesn’t bother me at all.