I’m expecting them to just use the multiverse angle with his prior films being their own universe. With the 4th wall breaking nature of the character, I wouldn’t look too much into it.Well, the time travel is canon, which means, if they do acknowledge them, the first two films, and thus the X-Men universe supposedly, are set in alternate timelines. Could retcon Cable's time travel device to being Quantum Realm related, explaining how the credits even worked.
If he goes back to his original timeline, using the same method from Agents of S.H.I.E.L.D. S7 and Avengers: Endgame, then I guess that the first two films are seemingly canon to the MCU, somehow.
All this means right now is Deadpool 3 is canon.