The MCU is one universe that is part of the Multiverse. It is parallel to the universe of Howard the Duck (who was in Guardians of the Galaxy). It is also parallel to the main comics universe, the X-Men movie universe, the X-Men cartoon, universe (and basically all the others in the Marvel wiki).
Parallel universes exist independently of each other. Remember, the Infinity Stones came from some other part of the Multiverse.
They introduced the idea in Doctor Strange so viewers will have at least a clue of what's going on if they reboot the whole franchise, or for example, they get the mutant characters film rights back, the X-Men stories have a lot of internal history, so if they get the rights back, they could either have the beginnings of mutants showing up, causing a lot of changes to backstories like Magneto, who've been doing their very public thing for decades.
Otherwise, they'd have to explain how no one had even heard of the millions of mutant characters, so I'd bet they'd either reset the whole universe so there were mutants all along, or they'd remind their viewers of the multiverse, and have the existing mutants come on over from their current Fox-owned universe, even played by the same actors.