i don't think the alternate wold is the human wold (cause is more an alternate equestria) they all have strange color and there are the alternate reality of all the mane 6....so the dubt is: where is alternate twilight??
i see this spin off a lot like naruto road to ninja , in wich there is an alternate reaity with all the protagonist.
then 3 thing can happend:
1) alternate twilight is somewhere in the alternate dimension and come at the school after the twilight from equestria come back. (like naruto and menma are alternate version and naruto take menma place while menma is elsewere)
2)alternate twilight swich place with her contropart (like sakura and genjutsu sakura in naruto road to aninja and naruto road to sakura episode) so while twilight is in the "alternate equestria with humans" her alternate version come in the original wold...when twilight come back the alternate come back too.
3)twilight take the place of her alternate so they are the same in that moment, when twilight come back she left the humen version in equestria gils wold (like tobi when take control of menma in naruto road to ninja)