It's canon that the Garlean 3rd Eye and the inability to manipulate aether are two different things. They just so happen to crop up in the same race. Raw skill at manipulating aether arrives from person to person as it is, it's just that the Garleans as a race can't do it easily. Until Zenos started messing with the Resonance that is...

The 3rd Eye apparently gives Garleans better spacial awareness which is linked to them being very good with understanding how magitek works. It probably also accounts for why they like airships and aerial combat. Interestingly enough, the other race biologically inclined to spacial awareness is the Au Ra (their horns process sound differently for a similar effect) and they also really like aerial combat as well.

As for the inability to manipulate aether... we still don't know why that is. The Ivalice raids have confirmed it is not a new development and has been around as a racial trait for a while though.