I maintain separate Apple IDs for my iTunes purchases and for my devices.
While that may indeed be the issue, syncing has never been a problem prior iTunes 12.
All my devices are logged into the iTunes/App store with the same associated Apple ID that iTunes is logged into with my Mac.
Apple doesn't require a device's Apple ID and iTunes store account to be the same.
iTunes doesn't have any issues syncing any other data to my devices, including music, only apps. I recently purchased an album on iTunes on my Mac, and it seamlessly transferred to my devices. Apps do not.
And, I can still manually tell iTunes to sync updated apps to my devices. It will happily send apps purchased via one Apple ID to a device "owned" by another Apple ID.
"it just worked" with iTunes 11 and prior.
Now, I am tempted to set up Family Sharing and see what effect it has, using my "iTunes" Apple ID as the master, and the devices' Apple ID as the members. But I am leery that it will muck things up even further, and beyond.