Judging from Harrison Wilcox's tweets, he was a exec producer for these shows, Earth-12041 and Earth-17628 had very similar histories but the differences make them exist as separate realities.
Think of it like the X-Men film timelines - they're extremely similar and COULD be simply interpreted as separate timelines within the same universe, but major inconsistencies like, for example, the characters' ages post-DoFP not lining up, like Jean's, lead it to a more complicated reasoning. They're not simply just alternate timelines, but they're alternate realities
with similar histories
but a few drastic details
that make them not same reality but a different timestream. But a whole different universe entirely.
Layman's terms: Kitty Pride phased Logan into another universe branch, not through their timestream. It broke off and created a universe with it's own history.
The MAU is more or less several branches with similar histories but with some details that happened differently that diverge into their own branches.