The costume discrepancies are the biggest hurdle to having DC and the current DCU timeline sync up for me.
For instance, the cover of DC#1 shows Superman in his costume without the underwear. But in the current DCU timeline he has his underwear and most likely won't lose it again.
And IIRC correctly Batman has the suit with the yellow oval in DC, but in the current continuity he has recently switched back to his classic black bat logo costume. I realize he could change it again, but it seems unlikely since he just changed it to that one.