Winning allies for the Alliance, one wiped-out monster invasion at a time.
I won't discuss the way Twilight and Cortana bonded at the post-massacre party. Suffice to say that everyone agreed that giving Twilight Sparkle access to an interstellar vilification's tech base was a quick way to destroy the universe.
I already agreed with that point. And I gave you the fact that they aren't in all those universes at once, because they are clearly only in one universe, as no one can occupy the same space in similar or dissimilar dimensions, because standing in your own footprints/hoofprints can have a negative impact on the multiverse at large. So, while there may be a group exactly the same as that one in differing universes that all correlate to the ones these heroes are from, they wouldn't be the exact some characters, and therefore, are only subject to the reality of a singular universe at a time.