OK I think I worked it out.
So with iOS 9, apps are distributed in pieces just for your device to save space and bandwidth.
Example: A universal game app that is compatible with iPad and iPhone
So on an iPhone 6 it installs the 64-bit version of the app plus the graphics and assets that fit and work on the iPhone 6 only.
On a iPhone 6 Plus it installs the 64-bit version of the app plus graphics and assets for the large 6 Plus screen.
On an iPhone 4s it installs the 32-bit bit version of the app plus graphics and assets for the smaller 4s screen
On an iPad Air 2 it installs a 64-bit version of the app plus graphics and assets for the full size iPad Air 2 screen.
So when you try to sync back to iTunes, you would only have just a pieces of the application for that one device you synced to send back to your iTunes.
I own both an iPad mini 3 and a iPhone 6 Plus. So if I only synced back the pieces of an app for the iPhone, then it would not work for my iPad or other devices.
Therefore iTunes on your PC or Mac really needs to download all the pieces of the app for all devices from the iTunes store so you can sync any device.
That's the way I understand it. I hope that makes sense.