Maybe. Simpler, certainly.
Look at it this way: how does the core concept of the X-Men benefit from sharing a world with the likes of The Avengers, Ghost Rider, The Inhumans, The Fantastic Four, The Runaways and Jessica Jones?
Because it reflects real racism and prejudice better. In real life, there are always minorities that get it worse than others and always some who aren't as good at co-existing than others for one reason or another. The X-Men having a harder time co-existing while others have it easier is worth exploring.
How much does this sort of thing directly clash with the "us vs. them" narrative that's at it's very core?
It doesn't, the Mutants just need to accept they're just one facet in a Universe full of tons of weird stuff and maybe they need to change the way they do things in order to find acceptance. This is a two-way street and the X-Men are infamously bad at their job of co-existence. This is mainly due to Xavier's incompetence, of course.
The X-Men's greatest weakness has always been their inability to run a good PR campaign. And the one time they really tried Cameron Hodge was running it. Still...
- Let's not forget all those years the X-Men hid out in their mansion going "No mutants here." Meanwhile Wanda and Pietro were in the Avengers a public group, publicly being mutants, and saving the world, and doing what they could to help people understand that mutants weren't all evil. Meanwhile to the public the X-Men were mutant assholes who go and fight other mutant assholes, get butthurt nobody automatically knew they were supposed to be the good guys. And then have the temerity to keep blaming the ones who were on the Avengers for how they didn't do enough or are race traitors after spending decades hamstringing their attempts to show the public that mutants are actually pretty cool dudes.
-Oh and the treatment of Wanda, they're hypocrites. Hey Look Jean's not the crazy Phoenix anymore, lets welcome her back and protect her! Uggh that Wanda did something mildly less genocidal, we hate her. Oh and don't care about it being the Phoenix not Jean, it was acting with Jean's memories and emotions, so yes, if it had been Jean, she'd still have eaten the sun of an inhabited star system, killing billions. And with far less reason to be mentally unstable than Wanda had.
-And finally again, publish your manifesto and goals to the public!. Magneto at least always announced who he was and why he was doing things. You just show up in masks and start shooting and being all secretive. If a bunch of guys dressed like cowboys start robbing someones house and some other group dressed like cowboys shows up to fight them, people aren't going to think "Oh this second group of cowboys must be here to save me!" They'll think "Why am I stuck in between these cowboy assholes!"