App Auto Update (Does it work now?)

Was fixed in iOS9.3. Works for our 1900 iPads now.

I asked Jamf support about this and was told that the feature will work for any devices that are on iOS 9.3 or higher, but it will still be broken for ones that are on iOS 9.2.1 or lower unfortunately. The issue was a part of iOS, so you could actually enable it with any version of the JSS that has that feature and it will work on the 9.3 devices. However, since you will still run into issues with iOS 9.2.1 or lower, they would recommend that you do not enable it until all devices are updated to at least 9.3.

My JSS is on 9.82 and automatic iOS app updates are working for me with users on iOS 9.3.