Because in the original story the Phoenix does inhabit Jean, the cocoon bit was retconned...
2 part answer... 1st part deals with the story itself, 2nd part explains the retcon.
It's my understanding that, in current canon, the Phoenix made a duplicate of Jean Grey to inhabit, and as you said the duplicate retained Jean's memories and personality, so in essence the body it inhabited was, for all intents and purposes, Jean Grey... just a copy. Like the Phoenix stuck her in a copy machine and saved the original. It's likely that, if the Phoenix as Jean Grey never died, and the real Jean Grey was found they would probably both believe themselves to actually be Jean Grey, and they would technically both be right... but only one of them would have actually lived the true life of Jean Grey, while the other would only have remembered it... So, technically this IS the scenario of Jean struggling to control the Phoenix. Two minds inhabiting one body, Jean struggling to stay sane and dominant, and the Phoenix eager to satisfy her curiosity. In The Phoenix Saga, the entity is moved by the positive emotions the Jean copy displays and her motivation to protect life and her loved ones. She goes bad in the Dark Phoenix Saga because she becomes aware of darker human emotions she didn't know about before and hungers to explore them. That hunger drives her to commit horrible acts, solely for the thrill and education of the Phoenix entity. So the Phoenix entity is not evil, but it isn't good either. It is simply a force of nature motivated by curiosity, it was motivated to do good because of Jean's "good emotions", and bad from her "bad emotions". It was really just an experiment for her.
However, there's another reason that the story is written the way it is, and it has to do with the real world, Marvel, and not the story itself.
Initially the story was going to be written with a different ending. In the story, the Phoenix destroys an inhabited planet and kills millions of innocent people for her own satiation. (Correct me if I'm wrong guys) Marvels editor at the time, Jim Shooter, advised Claremont to have the planet the Phoenix destroys uninhabited, but Claremont released the book without making the change. Claremont's original story would progress from there as it is in the book until the moments before Jean kills herself. Originally, after Jean's death the Phoenix force was supposed to bring her back to life (just like in the 90's cartoon version... which is actually the original story as it was written, sans Rogue and Gambit...). But because of Claremont's decision for the Phoenix to be a murderer, she had to pay the piper. Shooter felt "that allowing [Jean] to live after killing billions of people would not be fair." So she was killed. And to bring her back years later, the original story had to be retconned. Where originally Jean had been the one possessed by the Phoenix the whole time (where the story makes sense), NOW Jean was only possessed by the Phoenix for the short trip from the space station to the harbor, and then copied and put away for posterity (instant holes).
Hopefully that wasn't too confusing. LOL...
How'd I do guys?
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