I'm more speaking from the pov of someone who has heard the constant argument that things can't work before. All the arguments about retcons, character swapping, recasting, time travel, same characters in different franchises, aliens, magic, robots, crossovers, continuity not flowing well between movies etc the debates have always been off. Only fans think it will be an issue with audiences... and it never is. The audience is very accepting of all that but... they are fully aware about one thing with the A list X-Men. They are mutants. X-Men hit mainstream pop culture far longer ago then the Avenger crew. Ultimately they just want a good movie, but if we are talking about things they will quesiton, not making them mutants will be an obvious one.
Just as comic fans don't when they read the comics, audiences won't care one bit if there are Inhumans and X-Men. What audiences are willing to accept on the fantasy side of things is very similar to the fans with these mainstream comics. One side is just more obsessive and will nitpick 24/7. Whenever Marvel gets the full rights (which won't happen anytime soon) or Marvel and Fox make a deal (way more likely) and mutants are switched to Inhumans for good I will have no problem admitting I was wrong. But I am fairly confident that this will not be the case because it can work without issue. Look at how everyone was like QS and SW are gonna be Inhumans. Nope. They could have made them that, but they didn't.
Much like Spider-Man and Daredevil if Marvel had their hands on X-Men we will see a fast switch up and big focus on them. They won't wanna get them directly connected with another property when they can sell them as a completely new separate idea in their universe. That will be the sell. Would there be similar themes? Sure, Marvels playing those right now on AOS with Skye. They just flat out can't use mutants or X-Men so it makes sense for the time. But how Marvel handles the main Inhuman property will be very different then how they would handle an X-Men one. Inuhumans want to walk through that mist right now on AOS, and are more like a cult. Until Marvel drops a terrigen bomb on the MCU world this stuff isn't even in play. Mutants don't have a choice, so the same would have to happen with Inhumans. But even then, you can have a much different origin here for mutants then alien test subejcts that walk through a mist. World expansion has been a huge part of the MCU, can't see them wanting to cut it off if they have the chance to dive into potential new stuff. Especially with something as big as X-Men.