My Illogical Theory
Think about it - wouldn't it look a little weird that The Mountain Kalos Dex - the last sub-Pokedex in the Pokedex - doesn't have the legendaries last?
They just want to follow tradition, as putting them lucky last.
As another theory, if I remember correctly Xerneas/Yveltal was trapped and transported to underground Geosenge by Team Flare. So maybe where it actually comes from is a Mountain Kalos area? :o
Hope I helped. :)