This same thing happened with Superman Returns. It was made as an homage to the original Reeve series but became retroactively added to the same continuity. It causes slight problems but they can be generally overlooked because that was not the intention of that piece of work to begin with.
That line can be more or less disregarded. Logan was intended to be a standalone film based on the Xmen films so anything they did for world building is relatively redundant. Deadpool and Wolverine retroactively added it to the same continuity (more or less, branches or whatever), so we...
The Sentinels heavily appeared in the tie-in video game released alongside The Last Stand, as well as the video game adaptation of Origins: Wolverine. They were always about but never given any proper focus until Days Of Future Past.
Moira's comic mutant ability is the ability to reincarnate. It's possible that she did unlock her mutant potential after being killed in duty, therefore reincarnating into the woman we see in The Last Stand.
We can assume the X2 events happen before January 2005, or even 2nd November 2004 as President McKenna did not win the 2004 election, given the new president we meet in X3. Most likely a successor of the same party, but could be the opposing winner. I think October 2004 is probably a safe bet...
I had it that Stryker was using the site for secret experiments after the accident because IRL the site was still standing and not hazardously toxic but no longer operational until the mid 90s. Then the events of the film destroy the towers completely. Origins' impact on the timeline has always...
1994 would work because the Twin Towers are still standing in X1. However we know for a fact that X3 is 2006 and the ages for the characters wouldn't line up otherwise. They double down and say 15 years since Weapon X in X2 as well. Was it officially confirmed that Origins is 1979. I know that...
I always thought that it seems far too long since the last film. It would then mean the "events" of Origins now happened in 1991, going off of the "15 years" lines. I've always been in the belief that X-Men: Origins - Wolverine didn't actually happen as we saw it but it's how Logan believes it...