I always felt it was odd that Notch bashed Windows 8 so publicly for the store, yet happily sells on iOS, XBox, PS3, etc.
In the case of the latter it is well known and can be planned around. In the case of the former you have fully invested and then suddenly the game changes.
Applications from outside the App Store run just fine, as long as they're signed with a developer certificate. The certificate presumably costs $99/year, but you don't need Apple to approve your application.