Let me chime in here, if I may. Firstly, since you're discussing characters and a concept—Jean, Rachel, and Phoenix, respectively—that Claremont developed and created, I think it's important to note what
his past intentions and current vision were and are for them, especially since several of the writers that followed him have adhered and continue to adhere to both. Secondly, Jean's recent developments and established lore should also be discussed, particularly what was revealed throughout the
Jean Grey (2023) miniseries,
The Original X-Men #1 (2023),
Immortal X-Men #16-18 (2023-2024), and Gillen's recent interview with AIPT, because they all line up with Claremont's vision and intent.
That said, Claremont has always maintained, as recently as last year, that "Jean...go[es] on forever," referring to her as one of the "core elements of the omniverse" and an "omniversal constant" (see his 2023 interview with Near Mint Condition below; go to the 33-minute mark). He makes it clear that Jean—her psyche and being—transcends timelines, i.e., she is a "constant" across the multiverse, which becomes clearer to her and us as readers as she ascends. (Sidebar: There's a reason why, in Jean's thread, I recently suggested that her astral tryst with Scott in
X-Men #30 (2024) could have been the catalyst for Rachel's conception on Earth-818. That's because Claremont never saw Jean as having alternate versions of herself as much as infinite facets of herself.
Multitudes. But I digress.)
Since Claremont considers Jean an "omniversal constant," it's clear he envisioned
one Jean/Phoenix as the mother of
one Rachel. After all, they constitute temporal anomalies, both as individuals and as mother and daughter. Destiny herself referred to Jean as a "nexus of probabilities" in X-Factor, which Tom Brevoort recently stated "was a reflection of the fact that Jean was still the Phoenix, even if it didn't seem so at the moment." (2nd Sidebar: Brevoort's comment is telling, considering the fact that, at the time, Madelyne was being animated by the portion of Jean's psyche that lived through the Phoenix and Dark Phoenix Sagas and which Jean wouldn't reabsorb until
after Destiny's observation. Food for thought.)
In addition, Claremont expounded upon the Phoenix/Dark Phoenix retcon—he convinced Shooter to let him rewrite Byrne's original retcon—to reveal that Jean's psyche animated the "Phoenix clone" all along. He saw to it that Jean had always been and remained Phoenix/Dark Phoenix. Moreover, Simonson doubled down on this in
Jean Grey #4 (2024) when she had a facet of Jean's psyche tell her(self), "[Phoenix] rode your anger, your need, as far as possible...until your
true will asserted itself and stopped it. You
died, of course." (Sidebar #3: I also find it telling that Jean from
Age of Apocalypse was among her many facets in the preceding issue [#3], demanding that she answer for "creat[ing] this mess.")
Furthermore, Gillen's description of Jean and Phoenix's relationship in
Immortal X-Men #18 (2024), not to mention the dialogue he used to depict her scrambled thoughts in the previous issue, also adheres to Claremont's original intent and vision for her:
And when a fan asked whether Gillen's recent work on
Immortal X-Men implied that "Jean, the Phoenix, and the White Hot Room are one," he responded, "I would say that's an over-reach
from the present evidence. You stab a voodoo doll and it hurts its target—but it doesn't mean they're the same thing. It means they're connected, in some way.
Which isn't to say it [i.e., Jean, Phoenix, and the White Hot Room being one] isn't true either..."
Lastly, in
The Original X-Men #1 (2023), Gage makes it implicitly clear that, at a certain level of consciousness, there is no distinction between Jean's "alternate versions" when Purple Phoenix reminds Marvel Girl, "And there are other worlds where you—where
WE—did just that."
I wrote all of this to note that there is plenty of evidence, some of which I've cited above and some of which I've not, to assert that, at Jean's core, (1) she exists "out of time," (2) her relationship to and with Phoenix is unparalleled, and (3) her role as Rachel's mother is not compromised by alternate timelines and earths. Jean
is Rachel's mother.
Is it any wonder Rachel has never viewed her any other way?