> In Android, it is possible to use third-party stores or sideload apps.
In Windows Phone it is also possible to sideload.
> Or you can develop your own app totally offline.
You can compile .NET to native code via release builds, before deploying it to the Windows Phone.
It is only when you upload the appx to the store that MSIL is still used.
But I agree that with Windows Phone and now with iOS going bitcode as well, there isn't the issue of third party stores.
Still, nothing would prevent such stores to offer a server compiler service.