Yeah, the proper explanation is above, but all in all it did actually make sense, both in actual and metacontext. The problem was, even mentioned in the story by Simone, that Prometheus had been introduced as a significant big bad, who managed to pose a threat to the League of Gods. Then he suddenly dropped to jobbing for a lot smaller names. Simone tried to rectify the situation somewhat in her story, the taking out of Shiva and the Birds inability to defeat him, but the backstory was still there and problematic as it didn't fit the story. What made things worst was that even graphically the character didn't match, as in the original story there was a reason why his hair was white, yet in later stories, his hair was anything but white.
So they decided do the retcon by having an impostor act as Prometheus and although the story probably sounds confusing, it was actually relatively well written and made sense in the way it was presented.