We aren't taking Smallville continuity at all, other than part of Lex's backstory (the Julian bit as of Memoria, the meteor shower w/mutagenic rocks, and the existance of Excelsior) and Lois' as an army brat. We're using SV pbs, and I'm still discussing with our new Clark (she lives with me) how much of that she wants to take before the Man of Steel reenters the game.
So we steal from there as we please. As well as the DC AU and the comics.
Tim got sent away during the last blow up with the Joker, so he'd be understandably confused as to what was going on (and why Lex Luthor is kickin' it at Wayne Manor).