Sorry for the delay replying - I actually have precedent for the same person looking different in different universes in an earlier story; my version of Dick Greyson is a refugee from a comics-based universe, my Batman is the Batman Begins movie version. Dick mentions that in his universe Bruce Wayne is older and has been Batman much longer, and that Superman is also different.
My explanation for this is that there are a lot of universes - Tempus was targeting versions of Clark in very similar universes to the L&C universe, the further apart they are the greater the chance that things will go differently, e.g. Clark's ancestors over several generations were the result of different egg/sperm pairings and looked a bit different by the time Clark was born, the same for Lois.
