Originally Posted by
Omega Alpha
He didn't know everything. Moira already said Xavier could only see her mind once, and she wouldn't allow a second time. He certainly knew Magneto would show up eventually, but not details to make it inevitable. Besides, before the events of UXM #150, Magneto was too crazy and radical.
Also keep in mind that Moira said she tried to break Xavier into her worldview, and was implied Onslaught was a consequence of that.
There's also the fact there are many events that are unique to this reality. At the very least:
Onslaught
Proteus
Legion
AoA and everything that comes from it
Everything regarding Genosha (the origin comes from Sugar Man's experiments)
The Mutant Massacre (no Dark Beast experiment on the Morlocks)
The Xavier/Magneto/Moira split that came from Moira thinkering with him
There's likely more too.