It's ironic that Charles Xavier's Korean War service (along with his stepbrother's) is largely downplayed and ignored while Magneto's formative years in the Holocaust are not. They really won't be able to keep Magneto's origins fixed there for much longer-- he should already be at least in his nineties, and they have already cloned and/or de-aged him at least once.
These days they have miracle medicines on Krakoa plus a resurrection system that can reset people's age, so I think they're good. One of Krakoa's main exports is a drug that can take 5 years off a human's age, so who knows what sort of good stuff they're keeping to themselves?
Charles has also been cloned twice. The first was at the end of the Brood saga back in the 80s, and the second is a little more complicated. A few years back, when Cyclops had the Phoenix Force, Scott killed Charles. Some time later, Charles' mind returned in Fantomex's body, but then that body got killed at the start of the Dawn of X comics. At that point, they cloned Charles' original body and re-inserted his mind into that, so now he's back in his own youthful body.
Also, Charles' service in the Korean War isn't a core element of his character, the way Magneto's experiences in Auschwitz are. The temple where Cain became the Juggernaut and Charles lost the use of his legs could be anywhere — the Korean war was just the excuse for putting Charles and Cain on the scene, not important in itself.
Magneto's a little weirder, because as you say he got reset to early adulthood (let's call it 20 for good measure) at some point. In the comics, this was in the 70s, but on account of sliding timescale it could really have been in the 80s or 90s as well. So assume he's 15-20 at the end of WW2, which would make him about 65-70 in the 90s (old, but not so old that he can't be active), at which point he gets reset back to 20. That'd make him biologically about 50 now. If you put his reboot in the 80s instead, now he's pushing 60.
But age has always been a really weird thing in Marvel. The worst example is Franklin Richards, who was born in the 60s, canonically 5 at the time of Onslaught (mid-90s), and 8 from at least 2004 to 2014. Now he's been aged up to a teen, though.