I guess that depends on whether you see the App Store as a single shop, a department store, or a mall. There might not be Abercrombie & Fitch departments in Walmart, but there are certainly Apple-store-themed electronics sub-departments within Best Buy.
You got it. I think the sub-departments is exactly the wrong model. Completely separate stores with completely separate and unique identities. Apps not also sold in the app store. Boutique shops selling and supporting a very narrow vertical.