I just got off phone with Tier 2 AppleCare who reports this is an emerging issue, and he's not yet sure if:
A) it's a bug
B) the App Transfer is now "built in" to Back Up Now and that we simply won't see an indication that app transfer is happening.
If the latter, actually… with the multitude of new users over the years, unless I'm missing something, as a very long term user myself, I always wondered why did Apple feel the need to indicate that the transfer was happening, when after all, it is data that that like any data should be backed up in a back up. If you have used iTunes for a long time, in the early days you had to Control click Backup to get a drop down menu with Transfer, Sync and Backup. AppleCare was always fielding calls about what was the diff between Sync and Backup and then that difference disappeared from the process so when you backup or "Apply" a change, iTunes syncs and backs up all in one. So… it seems logical to me that App Transfer might be built in as of iOS 9. To me, it would make sense and be fine with me. But we do need to know that Apps are in fact being backed up. Although.. as most here know, all our apps are listed in "Purchased" so if we have to restore we can clean install and simply go to Purchased and download the Apps we want, which for me the times I've done this, I always change by list of Apps on a clean install for the ones I've stopped using and no longer need. So worse case is apps are NOT being transferred, but we do have a very viable solution if Restore isn't complete.
So while not a complete answer to this thread, just know Apple is aware of the app transfer issue and we just need to know if App Backup is built in and we're not being advised during a backup that the transfer is happening, or that it's a Bug and apps are not being transferred and a fix is in the works. The Tier 2 rep said he'd call me back when he had word which. If he does, I'll post what I learn next.
Hope this helps.
Steven