Technically Batman/Superman #3.1, the issue will tell the tales of a number of different Doomsdays, whose designs vary slightly and whose stories may or may not have actually have occurred in the rebooted timeline of the New 52.
One such story, apparently, is the Death of Superman, which Pak won't answer directly whether it still "counts."
In the previous timeline, Doomsday was a Kryptonian biological weapon--a being engineered through rapid, forced evolution to become immune to harm. Perhaps unsurprisingly, some memory of the billions of years of trauma he suffered over the span of a lifetime stuck with his biological memory, informing his survival instinct and turning him into an uncontrollable, destructive force.
When someone finally defeated Doomsday, he was tethered in the strongest bonds they could forge and shot out into space in a powerfully-reinforced box, inside which he "hibernated" for hundreds of years until he woke up, battered the Justice League and killed Superman.
The Death of Superman story was one of only a handful of old stories that has been consistently referenced by DC Comics as having occurred in the past of the New 52, and Grant Morrison even referenced the story during his Action Comics run. Still, being told off-the-page that something "counts" is not the same as seeing it play out in front of you--just ask Tim Drake.
"A little girl asks her father about this terrible monster named Doomsday. And the two of them trade scary bedtime stories. And then the other shoe drops," Pak told ComicsAlliance. "The stories are narrated by the father and the daughter, who of course may have their own reasons to tell the stories the way they do. And yes, the father and daughter are key DC Universe characters of special interest to Superman fans."