I would HAVE to think Crisis on Two Earths and JL: Doom are set in the pre-Flashpoint timeline.
For starters, there are only 3 Earths really in CoTE - Earth-Prime, "Earth-1" and a "Earth-2" that resembles Earth-3 from the comics.
1. The frozen wasteland Owl Man died on could be just be any other planet in the 3 universes.
2. Most importantly, the Crime Syndicate Earth CAN still exist without much of a multiverse. That being the antimatter created universe, sort of it's own thing apart from the Animatter Universe, from this storyline the movie was based on:
https://en.wikipedia.org/wiki/JLA:_Earth_2
Then the Tomorrowverse sparked the animated Earths as we know it, created a new Earth-2, shifted the Crime Syndicate Earth up to Earth-3 and rewrote that timeline - then Crisis happened and we have the multiverse that's introduced to us via the DCAU (post-JLU) and My Adventures with Superman.
@Pro Bot