Also, Jon does remember her, his question is a response to the word "her" - meaning that he's clarifying who "her" is as that's rather ambiguous.
The "this world's version, yes" is definitely "new reader fill-in". Tends to be kinda clunky in comics, but really not that big of a deal.
Then the "wow, she looks just like you" part I took as the pictures reminding Jon (and him reminding the reader) of just how much she looks like his mom as opposed to him now knowing (New52-Lois did meet Jon, after all - but either an "I still can't get over how much she looks like you" or using "...." at the end of the sentence instead of the exclamation point would have conveyed that better.
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