Yes, the Phoenix being a separate entity from Jean Grey was not part of the original story. That was retconned later, in X-Factor, I believe.
Originally, it was Jean Grey whose powers "awakened," and she took on the Phoenix persona. Then she went nuts, started killing billions of aliens, and was killed on the Moon. That was supposed to be the end of her character, then it was retconned away by saying the Phoenix Force replaced her and left the real Jean Grey in a healing pod under the sea (something like that), where she was later found and joined X-Factor.
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