It’s been this way since Friendship is Magic, Season 01.
I don’t think so. What episode was this established in? It was definitely true since Twilight’s Kingdom.
As a side note, I’m not really a fan of the idea. If a creature has wings, it makes sense to assume its ability to fly comes from having wings, rather than from magic. Narratively, you could have achieved the same effect by saying that Tirek stole their ability to control the weather.
Anyways, if they play up the irony angle I brought up earlier, then it kinda works out.