Eventually, I hope that they clarify this. But based on what we've been shown so far, I think that other than the three universes that combined -- Earth-1 (Arrow, Flash, Legends), Earth-38 (Supergirl) and Earth-73 (Black Lightning) -- all of the other Earths were simply recreated as they were.
In both pre-Crisis scenes and the closing montage of the crossover, we saw the Titans universe labeled as Earth-9 and the Christopher Reeve/Brandon Routh Superman universe labeled as Earth-96.
So until they actually explain to us that the multiverse is truly different, other than the three universes that combined into Earth-Prime, that's what I'm going with. Heh.