Disclaimer: I don't own any thing if my own character.
This is my take on Superman returns…
Prologue- Slight change in Superman return
When Perry ask Lois to do an article on Superman and give Clark the robbery Lois wasn't very happy. She doesn't have the time to take with Richard about Superman. She goes on the roof before they got the chance to. She was found by Superman on the roof and the rest of this story goes like the movie. Since the conversation on Superman / Clark similitude never happens (in my story) they never almost put one and one together.