I'm pretty sure this wasn't brought up as a concept, but if it was, I apologize.
When looking at the parentage of alt-reality or alt-future offspring, like Rachel and Nate, we need to look at the point of divergence between our reality and the one in question. Because of how divergence of realities works, then we can safely assume that two individuals who existed before the divergence point are the same in both universes. 616 Magneto and 295 Magneto are genetically the same person, conceived and born when both of these universes were one. The divergence point between Earth-616 and Earth-811 was depicted in the original Days of Future Past comic, so all of the adult X-Men were alive and well, including Scott Summers. And I think it's fair to assume that many other actions, like the return of Jean Grey in the "Phoenix Rising" arc are independent of the DOFP outcome, thus bringing a genetically identical Jean Grey back into both 616 and 811.
It gets a little bit more tricky when one is NOT born before the divergence point, but are close. Consider a character like Scott Summers in the Age of Apocalypse. The moving timeline of comics makes it hard to call whether Summers was alive when 295 diverged from 616, but if he was not yet born, then he'd be along shortly. Given that most of the interesting characters in Earth-295 are of reasonable ages, given they exhibit the same physical features and mutant powers, and given that there was some delay between when the universes diverged and when Apocalypse actually started affecting things (meaning that Christopher Summers and his wife would've had sex the same time in both universes, as no significant outside force would've affected that), the end result is genetically identical characters. I'm happy positing that had a different sperm been the one to fertilize the egg, Scott Summers would've looked different, and maybe even had a different powerset. So once again, people that are genetically identical to your parents can effectively be called your parents.
Now, this rule would not apply to characters born far from the point of divergence. That we have very similar characters with the same names and powersets in weirdly different universes, like the Ultimate ones, does not relate to this issue. The hypothetical child of Ultimate Jean Grey and Ultimate Scott Summers would not be able to claim to be Rachel's sibling.
Caveat: I've read the entire AoA, but very little of the story of Rachel Summers, so if I'm off on some things, please school me.
</essay on the genetics of fictitious people>