Initially they were from Convergence transplanted to New 52 Earth-0, but from Rebirth onward it's rewritten so that the Super family has always been on Earth-0 and he was born after Clark and Lois married after Death of Superman (Rebirth continuity).
In Rebirth this wasn't much of a problem because the entire Rebirth story is about fixing the timeline, so some inconsistency can be part of the story.
This time though, time and space are supposed to be healed. Jon's birth was marked 12 years ago after Death of Superman, but according to Dick's flashback in Dark Crisis, Tim's already Robin at the time. If that's the case, everyone would be too old by the time Jon hits 12 years old, even without the age up. Tim would be 26 now.
One solution to this is Dick retelling Jon the event of Death of Superman based on memory of his past life in Post Crisis, instead of what actually happened in the current timeline.