The Red Thunder
Backwards thinking?
I like things being proper and tidy, sue me
I can't look it up now but I'm pretty sure in FRLG Bill or Cello (the trade guy in the Islands) mentions something about Hoenn and how they're basically at the same time. The time-capsle and pure references in GSC ensure it is 3 years ahead of RBY. I also believe their is a link between DPP and HGSS but again cannot look it up atm. Feel free to find and correct me but I do believe there was in-game references to the timeline being parallel or at the very least, damn close.
But, at what point in Kalos does it say that it exists outside of any other timeline?
And, if it does, who's to say that GameFreak doesn't perform a minor retcon to explain the ability to use MegaEvolution in Hoenn games? They've done retcons before, in the Third Versions and in future games. Case in point, Cyrus using Giratina, as opposed to Palkia/Dialga and the whole Distortion World thing. Scott following Brendan/May around Hoenn because he's recruiting skilled trainers for the Frontier. Red getting Pikachu as opposed to the starter. Eusine chasing Suicune around Johto, as opposed to Suicune being a standard runner. The supposed "inability to evolve Golbat into Crobat" because of some deus ex machina, until the National PokeDex is obtained in Fire Red and Leaf Green.
Trust me, if they want to make it so, they'll find a way to explain it, even if it makes little sense.