A really weird thing about the Joseph story in 90s X-Men is that everyone is constantly thinking, like, "Could our greatest enemy truly be reformed? How strange to fight alongside him!" But Wolverine, Storm, and Rogue were all members of the X-Men with Magneto in the late 80s, when he was the headmaster of the school, even. I understand that it was harder to get back issues back then and you can't expect every writer to keep track of years of continuity, but it really feels like most everything between the Dark Phoenix Saga TPB and X-Men #1 (1991) was memory holed during this period.
It's especially odd because there are significant connections to the Mutant Massacre in both Marrow and Gambit's stories in this era, and that was a period when Magneto was on the team. So you have these invocations of a traumatic event everyone remembers when Magneto was on the team, but then you'll have characters be like, "I can't believe Magneto is now, for the first time, part of the X-Men, who could have thought!" either from someone who this isn't actually new to because they were there or from some dumb-dumb from the original five who was tricked into pretending to be a mutant hunter while Magneto was holding the X-Men together.
To a lesser extent you also weirdly get this with Wolverine, where so many characters' relationships to Wolverine seem to be modeled after Cyclops and Wolverine's relationship on the 90s cartoon. But, even moreso than Magneto, Wolverine has been so much more of a core part of the X-Men than say Iceman or Archangel. If anything, at this point in time, everyone from the Original Five but maybe Cyclops should essentially be in the role of outsiders, and Wolverine, Storm, and maybe Rogue are the closet thing to core, stable members of the team who held things together while the going was tough.