"Empty, hmm? It does not seem devoid of life to me."

Yes, he does know what Starscream actually means by empty. Jetfire is being difficult on purpose. They both know it too. This situation isn't what he expects it to be. Jetfire doesn't like puzzles that don't have an actual solution to them. It's likely that he's going to be wracking his mind over this for a while before getting frustrated with the temporal elements of this matter and whatnot.

"I would have to think that somehow I didn't die. You can't bring people back to life, Starscream."