I think it's just as possible that Claremont is writing a flashback involving Slym and Redd or Cyclops when Nathan was a baby.
"We come into this world alone and we leave the same way. The time we spent in between - time spent alive, sharing, learning together... is all that makes life worth living." - Jean Grey
Yes, X-Men: The End/GeNext and X-Men Forever were set in different timelines.
In The End timeline, Jean died again just as she did in New X-Men #150, and Scott and Emma formally got together. Eventually, they married and had kids.
In the Forever timeline, Jean and Logan began a romantic relationship in X-Men Forever Annual #1, set before X-Men (1991) #1. Logan was then killed by the Storm clone in events set after X-Men (1991) #3. Jean telepathically feels him die, and the trauma causes her to start manifesting Phoenix-level powers again. In the course of this, Scott learns about Jean's affair with Logan, and he and Jean formally break up. Oddly, Scott later delivers the eulogy at Logan's funeral.