It's really not confusing at all.
Stryker's Team X never happened since Mystique likely screwed with his plans. Stryker did manage to get Logan into the Weapon X program against his will anyway (he volunteered pre-Days) and made him an animal.
The entirety of Deadpool could be explained as Wade's life post-Days. He never got put into Team X for his fighting ability, so he ended up a vigilante for higher in his own movie.
Days is the nexus point. Anything after that is the new timeline.
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