You're overreading into this too much, and it's ridiculous. The comic book continuity is MESSY as hell, especially when coming to the crappy "Phoenix Force" concept they added later on in order to launch the redundant and shoddy X-Factor title. In the Foxverse, original timeline(s), "PHOENIX" was the alternate personality of Jean Grey - generated by Xavier's heavy mental blocks over the years. In the original timeline, Jean ALREADY displayed the "firebird energy signature", because that is his natural mutant power. Period. "The Last Stand" established it, canonically. Like it or not. There are several hints in X2 too, however. In the new timeline, she never developed an alternate personality, because Xavier's mental blocks were VERY limited. He just suppressed the memories of the car incident and her father's refusal/repulsion. She absorbed the "shapeless" Cosmic Force, and the Force became one with her and her Phoenix power. That's it. She did not develop any alternate personality, but she was driven "insane/out of control" by this unlimited, infinite power. Much more in line with Claremont's continuity and original intent back in the seventies, right? Right. She is Phoenix. She has been Phoenix since "Apocalypse" occurred. Case closed.