Now that iOS 9 uses app-thinning, apps downloaded on an iOS device are not transferred to iTunes during a sync. They are also not transferred when you click "Transfer Purchases", so there seems to be no way to have copies of your apps you download on your iOS device in iTunes other than by downloading them all manually in iTunes.
In previous iOS versions, you would restore an iPhone by first syncing the iPhone with iTunes to copy all of your apps to the iPhone, then restore from backup (iTunes automatically did the first step for you). Now that apps are no longer copied from your iOS device to iTunes when you sync, the apps are not available for you to copy from iTunes during the initial restore sync.
My question is, how does iTunes restore app data for these apps when it doesn't have the binaries backed up? Does it automatically download them from iCloud, or does it not restore these apps (as was the case in previous iOS versions)?