The answer is it doesnt make any fuckin sense.
Logan was literally a movie in the DP universe in Deadpool 2. Deadpool even mentions it.
Deadpool 1 has the "McAvoy or Stewart? These timelines are so confusing" joke when Colossus comea to collect him.
DP2 clearly shows the McAcoy timeline characters.
Logan takes place in the Stewart era, meaning having it happen between DP2 and 3 makes no sense, especially since Colossus and Negasonic are clearly still alive in 3, and not nearly enough time passes between DP2 and 3 to make that possible.
The whole movie is riffing on how multiple timelines and multiverses arent working, are way too confusing, and dont make for good stories. The fact the continuity is so fucked up in DP's universe is just par for the course.
Doesn't take a lot of brains to be a good fighter.