"Bard, in the comics it has been shown that Rachel is the result of Scott and Jean...Yes, Claremont wanted Phoenix to asexually produce Rachel, but it didn't happen that way..."

Sinister's examaination of Rachel's dna did prove she is Scott's daughter in the comics. However, that doesn't change the fact Rachel was designed with this in mind, and therefore a "clone" of Jean. Basically when Jean was killed off, Marvel couldn't keep Phoenix out of the comics or else they would lose the right to the trademark if not used in a certain period of time. If they wanted Phoenix bacl they should have brought Jean herself back, and instead of giving Jean a daughter she never had.