This should solve a lot of the issues in making sure everything is connected, as separate universes ensure certain franchises can canonically remain separate until Marvel decides otherwise.
There’s still plenty of opportunity for things to get messy, but the MCU has been pretty solid thus far, so perhaps there’s no need to start doubting now.
Of course, Marvel seems to have a plan in place for this problem already, and is already introducing the multiverse into Spider-Man: Far From Home.