The Thor comments/confusion come I think from both Claremont and Cockrum's comments regarding Jean as this new Phoenix character. Here are both of their thoughts:
Claremont
“Phoenix is actually Marvel Girl at her ultimate extent,” Chris Claremont explained to The Comics Journal. “Phoenix in X-Men #108 (1977), when she saved the universe, was Jean Grey achieving her fullest potential as an entity.”
“Our intent was to create an X-Men analog, if you will, to Thor – someone who was essentially the first female cosmic hero,” Claremont revealed in Phoenix: The Untold Story. “We thought at the time that we could integrate her into the book as well as Thor had been integrated into the Avengers. The problem with that is that it grew out of the synthesis between Dave and me. The fact that we had, in a sense, created her gave me a degree of involvement that (artist John Byrne) didn’t have, coming in seven issues later.”
Cockrum
“When we first introduced Phoenix, we wanted her to fight Thor or the Silver Surfer, but (new Editor-In-Chief) Jim Shooter wouldn’t allow it,” Cockrum told Comic Creators On X-Men. “He said no female is going to beat Thor or the Silver Surfer. We kind of sneaked around him by sending her up against Firelord, who had once fought Thor to a standstill. We established her power levels that way.”
Cosmic or not
Cockrum
“Actually, when we introduced Phoenix I don’t think we intended for her to keep super cosmic powers, because the rest of the group becomes superfluous then,” Cockrum told The X-Men Companion. “Chris had said something about using the power to save the universe in X-Men #108 (in 1977), but that wiped it to such a degree that it reduced her powers. And after that, theoretically, she was not supposed to be that super-cosmic person.”
Claremont
“So anyway, we were told, Dave and I, that Phoenix could not be cosmic,” Claremont said in The Comics Journal. “And when the editor passes down an edict, you’re stuck with it. We had to cut her back. So we decided to cut her down to roughly where Storm is, which is fine. Now I had to think of a rationale.”
“The potential to become Phoenix is still within Jean. But without the necessary increase in her awareness, in her perception. If her consciousness, her soul, whatever, is not enlightened – if her consciousness is not cosmic, then she can’t handle the power. It’s like Doctor Strange could not become the Sorcerer Supreme until he had achieved a certain psychic and emotional balance, or awareness. Neither can Jean. She’ll burn herself out, she’ll be warped, twisted, turned into an evil person. Ergo, what happened was her mind shut her down, as a safety mechanism. To prevent her from hurting herself, it just dropped a wall down.”
http://secretsbehindthexmen.blogspot...ad-to-die.html