Being installed by Apps doesnt mean you can't then let the app handle its own updates. Play Services and Play Store are installed via Apps, but letting Play Store handle self-updating is fine and even recommended.
I guess Graphene could edit and make their own build of Accrescent to disable self-updates, and only serve updates through Apps, but that would be counterproductive because you'll get faster updates from the developer themselves, and dealing with building and publishing updates themselves is work for Graphene that isn't really needed.