>>21608955If by "recently discovered" you mean known by the majority of the Kalos region and possibly the world before the beginning of your journey there then yes it it was "recently discovered".
Seriously though, they never say that in game it was just how they marketed it, in game they've been studying the how it works for years without progress. Also it's perfectly reasonable for their to be "new" mega evos in hoenn because there are different pokemon not native to Kalos there and whatever event cause the megastones to be created clearly affected the world.
One more thing, the origin of mega evolution is going to be a story about the first recorded use of it not how it works. Unless you actually think GF has an idea as to how they're going to explain it.