i wondered if lex had just changed the story in his own head, to protect his heart.

Well, of course! But honestly, even without the Clexy reading of that scene, I think what Lex really wanted about Clark in s1 was his parents. The Lana thing is pure retcon. With the Clexy reading--well, he wanted to be Clark in the way that Tina Greer wanted to be Lana in s1: as part of repressed homosexual longings she was unable to articulate yet!