>>27510956They'll still be included in some form, even if they aren't expanded upon. They're too big (no pun intended) to remove, so expect them to be in even if they're locked to post-game. Besides, I'm pretty sure the Z-Ring has a slot for Mega Stones on it somewhere.
Going back to OP's point, the same logic applies. Alola Pokémon are like different ones altogether in terms of moves, stats, typing, and certain characteristics.