Yup, this is exactly one of the reasons I hate multiverses where there’s a universe where every possible story happens.
Multiverse of Madness was a mess, but it was my understanding that the Stewart/Xavier we saw wasn’t the same Stewart/Xavier of X-men, X2 and X3.
To add to your “few exceptions”, absolutely nobody has referenced the GIANT HEAD STICKING OUT OF THE OCEAN that Eternals established. I think they’re hoping that if they don’t reference something that we’ll forget it happened.