And frankly, a lot of editorial didn't want to reference Crisis at all and if it was a choice between not indulging the elephant in the room or indulging it, a lot of teams chose the former over the later.
And considering how messy the Pocket Universe and other stories that tried to explain things got, can you really blame them?
But anymore, I think it's a given that the current Supes isn't the Pre-Crisis E1 version and that guy lives on his own Earth. Mostly because you got stories like Convergence that now state that COIE never happened and you even had the Peter David Supergirl storyline "Many Happy Returns".
Which, for those who don't remember, had the Pre-C Supergirl get sent to our Earth, where Linda Danvers decided to try to spare Kara her fate of dying by taking her place in the Pre-Crisis Universe. Which had her marrying that version of Superman and having a daughter with him (which was heavily implied, if not outright stated, became the Supergirl of the 853rd Century aka DC 1 Million), until it all got undone because Kara not dying had some universal implications.
Thought that the intent of the New earth Superman was to have him as really being E1 version, but morphing into current one?