Nobody will care if Magneto goes from WWII to present day as a young man, that's pretty easy. How he goes from WWII to present day in a world where nobody knows about mutants, so there's no terrible thing being done every 5 minutes to justify his views on humanity, that one might be harder.
Yeah, it's vital that mutants are hated and feared and it can't be justified. It needs to be an irrational fear that turns violent, something that would make the introduction of the Sentinel Programme seem "reasonable".
One thing the original Fox X-Men movies were actually pretty good at was showing why the average person was scared of mutants (anyone could be one or become one, the powers were often hard to control, the news often focused on bad things happening because of mutants) and how government organisations used that fear and manipulated it for their own ends.
You need that. You need Magneto to have a point, to know what happens when the people in power decide a minority group is too dangerous to be allowed freedom. He and Charles need to agree that something needs to be done to allow mutants to live in peace, but they need to differ on what exactly that entails.
Personally I think the use of Krakoa and Moira McTaggart is the way to go. Not only would Krakoa give mutants a very distinct visual identity in their movies, but you can totally use Moira's mutant power to explain how and why mutants have been hiding.
You just say she has lived her life many times, always trying to find the right path forward for mutants. Simply say she has seen humanity turn on mutants, Avengers turn in X-Men, even Magneto defeating Thanos and claiming the Infinity Gauntlet for himself and wiping out all non-mutant life on Earth, which doomed it.
Then you just say mutants have been living in peace on Krakoa for decades, staying hidden thanks to Xavier erasing any memories anyone ever has of mutants, even when a kid manifests new mutant powers. Despite objections from Xavier and Magneto about hiding, Moira was vindicated when Krakoa protected mutants from Thanos but something has happened that means they can no longer hide.
That'd be a pretty great way to get humanity to go "what the fuck?" because nothing would piss them off more than being told Xavier has been fucking with their memories
for decades.