Original/retroboot
So each Legionnaire would consider themselves lacking in superpowers, but be able to do something none of the others can. And in the case of Karate Kid he's able to do karate well enough to fight Kryptonians on equal footing. Something humans can do in the DC universe, but none of the aliens can.
When Superman visits the Legion he gets hypnotized to forget the future, to prevent time paradoxes. He also forgets that Mon-El has been released in the future, so he keeps trying to cure him in the present. The guess is that on some subconscious level he remembers that Mon-El gets released in the future, and this subconscious memory prevents him from creating a permanent cure.
It would require post-hypnotic suggestion for the one or two instances where his remembering 1000 years was relevant to the story (like with Lady Memory).
For instance, Adventure Comics #4 has a scene where he's trying to find Adventure Comics #5, which hasn't come out yet. Because of Comic-Book Time, that scene happened more recently than it was published—which means it happened after Adventure Comics #5 was published—the story is no longer possible.
Legion of Three Worlds had him being sent to Earth-Prime where his friends and family were afraid of him because they read the comic books showing what he did. Because of Comic-Book Time, those comics now showed what he did years before he did it. This not only makes the scene impossible (unless they suddenly went scrambling for back issues and Superboy-Prime, a Legion fan, neither read Legion of Three Worlds when it came out nor had his friends and family show it to him), it also raises the question of whether he's actually responsible for his own actions, or whether comic book writers cause things to happen to characters in other universes.
- First, this would go to explain Prime's
Character Derailment in Teen Titans #97-100: despite the attempt of redeeming his character, he's back to his Jerkass Invincible Villain traits. Perhaps that wasn't Prime himself, but the writers controlling his actions. Secondly, it explains why the Anti-Monitor, Black Lantern Alexander Luthor and numerous other Earth-Prime crossovers haven't impacted it in the slightest-after they're done, the effects they've had on us are wiped out and we remain under the guise that they're just fiction. Given the Threeboot, this also includes our future. We may have been better off with Superboy-Prime killing off the DC writers...
It makes perfect sense—we're never told what the Klordny Festival is celebrating, and Miracle Monday is celebrated without any knowledge of why.
When Supergirl left the Threeboot, she never returned the flight ring. Lightning Saga mentions that Supergirl (Kara) has a flight ring, and one similar enough to Retroboot ring that it can be detected as a Retroboot ring.
Supergirl (Volume 5) Annual #2 has her joining the Legion pretty much according to the Silver Age timeline—before flight rings. Most writers seem to forget that flight rings didn't always exist, but it is taken into account in some modern Paul Levitz stories so it does still seem to be true. Therefore stories which show the Legionnaires always having flight rings are mistakes. If Supergirl had the Threeboot flight ring on her when she was taken to the Retroboot, it would have changed the timeline by showing the Legion flight rings before they had them. Brainiac 5 could then have analyzed the ring and the Legion would have flight rings without having to invent them.
Reboot
Very simple reasoning: one sent to the past (Phase), one in the present (Apparition), so the other one logically would have gone to the future. If the Reboot ever gets their universe back, except a baby Tinya to be appearing out of nowhere any day now.
Threeboot
The big piece of evidence that it is is that Threeboot Kryptonite is able to harm Superboy of Earth-Prime. However, we previously saw that it was able to harm Supergirl, and she's not from Earth-Prime.
- The Threeboot is a Hypertimeline of New Earth's future.
- That wasn't Threeboot Kryptonite, that was a strain of Element Lad created Kryptonite. He may have just been able to whip up some Earth-Prime Kryptonite. That would leave the issue open with the Legion-fandom as avid readers of seemingly Earth-Prime comic books.