Apple does have more registered developers than any other company right now. It is why Apple is able to get a larger portion of the consumer market than other devices even when they arrive late. Just take Apple's Watch and it's competitors for instance (Android wear and Microsoft Band).
What does the current state of the various app stores have to do with AR? By that, I mean, AR applications are so fundamentally and significantly different than 2D apps that back catalogs are meaningless. Any new player to the AR ecosystem is starting with an essentially empty app store, regardless of whether or on they deploy it on top of a pre-existing, successful app store. We can effectively say that Microsoft has the largest AR app store in the world.
And, we can expect Windows Store to grow as they push Windows Holographic and their tethered, cheaper VR displays (the Hololens is still a $3000 "dev kit"). Apple is not just starting from behind, they haven't even started yet.