I'm looking at this from Android, as that's the initial target and discussion here. If I download an app from Google's app store, I have some confidence that the app is well behaved and has been checked for obvious malware... But if the app depends on remote code that can change when it likes, how can I ever be confident in using that app and granting it permissions?
In the Dart Conference talk, they mention that sky apps (DART apps on Android) are given access to ever permission the system gives them.
These system given permissions will almost definitely work in the Play-store way (as opposed to asking whenever it is required, a la website style).