How was the foundation of X-Factor affected by this series?
Everything before (adjectiveless) X-Men #3 should still have happened, so it shouldn't have been. It's possible there's an untold story here, possibly the same one that explains why Cyclops's dad is in Alaska instead of starjammin' it.
Also, given your love of New Mutants, you might be interested to know, if you haven't already heard, that Claremont will be starting a NEW MUTANTS FOREVER series. Similar precise, leading off where Claremont's last issue of NEW MUTANTS ended.