That's always been the case in the comics for decades. There's timelines, multiverses, and all manner of in-between.
Spider-Man 2099 is from the future, but also from a different universe.
Aunt May (Character) - Comic Vine
Return of Aunt May - Peter believed, once again, he lost his aunt forever. But Peter quickly discovered the truth. May was alive. Indeed, it was Norman Osborn who kidnapped May. He replaced her with a fake May who was, in reality, a genetically modified actress. When Norman became totally crazy, his former employee Alison Mongrain and Robbie Robertson revealed to Peter where was his aunt. Peter saved her and defeated the Green Goblin. There are still questions: What did the Green Goblin had done to May? Is she the real May?
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IMHO, it's easier to see how far comic writers will stretch anything possible to keep a story, any story really, going by looking at a few character summaries.
Only then can you see the timeline of what ends up being usually a pretty bizarre character arc. I mean I get it, the writers of these comics are often boxed into a corner and don't have a ton of new characters they can just force into a legacy universe, but it starts to get less and less "grounded" as time goes on.
If you ask me, basically every "hit" show on Showtime ends up like a comic book ( Weeds, Shameless, Homeland, Dexter, Billions, etc, etc) where the last third of the show's run goes into just ridiculous territory and everyone had decided to mail it in and keep cashing checks.
If we all live long enough, we'll find out Aunt May was a member of MI5 and did wetwork with the Howling Commandos in her youth.
So here's the thing, the MCU can tell whatever stories they want to tell. They just can't be boring. That's where this show kind of grinds to a halt. Loki is just often very boring, and his fun factor was built upon never being a dull moment. Just some thoughts.
