The line from Stark which has gone around the most recently might as well fit on the Mutants now. The changes in the past made the present better but led to similar circumstances again.
It is also I feel the absolute point from which there was never no return which Ancient One tried to explain Strange in his episode from What If...? Season One.
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Not the McAvoy one that movies pick up from after, but the one we see at the end at Xavier Academy.
I believe originally (and assumed) the time Logan returns to is an alternate one of the original fox movies and the McAvoy timeline was a new direct timeline where they could do new things with the charscters without it contradicting the original movies a la Star Trek 2009.
I think the Doomsday X-Men will be from that alternated timeline Logan returned to. It gives them the freedom and clean slate to modify whatever they want for the movie without needing to adhere to the already confusing continuity of the x-men movies, and based on the ending of The Marvels, it looks like that's what's going to happen where they blend the comic/cartoon version of the X-men with the iconic og fox movies and actors.
You are right though that they likely will never clearly address it. I do strongly believe there will be confirmation that Deadpool is from the same universe though, as established in Deadpool and Wolverine.
Then again, Deadpool canon always has a * next to it as his stories are never really considered hard canon as they play loose with continuity and put it aside for meta jokes both in the comics and movies. Plus Deadpool himself is not a reliable narrator at all. An example of this is in Deadpool 2 where we are briefly shown the McAvoy X-men team hiding from Deadpool in the mansion, but timeline wise it doesn't line up because they look they look the same as they do in the 80s/90s but Deadpool 2 takes place in the present. Thats because it's just there as a gag. I heard someone best describe it that "if Deadpool is the narrator of a story or it's from his perspective, Family Guy rules apply where continuity is fluid and not the priority over jokes."
They could retcon it and have Deadpool be from the same universe as the Doomsday X-men, but since Deadpool and Wolverine's involvement is hinted to be more with Secret Wars than Doomsday then it probably would make sense to have Deadpool and Wolverine be from an alternate universe seperate from the Doomsday one, especially since that Wolverine is from a completely different alternate universe himself.
We'll just have to wait and see