Now that time travel, branching timelines, and wildly different variants of characters and worlds are an established part of the MCU, they really should just lean into the loose canon philosophy that Doctor Who has embraced.

That is, something is canon if it is useful to the story you are currently telling. If it contradicts that, then it is still canon, but took place in a different history that has since been altered or superceded by what’s happening now. Or it was a different timeline altogether.

Just tell good stories, and people will forgive canon slippage.