constant popup: "iTunes has found purchased items on the iPhone "xyz" that are not present in your iTunes library"
I was having the same problem.  When I looked a little more closely, I found I had checked that I wanted "Selected Books" to be synced.  For the three books I had checked as ones to sync, I am now showing multiple copies (10 copies in one case) in the iTunes Books sync page; although there is only one copy of each when I look in the Books app on my iPhone and Mac Mini.  Since I have my Books app on the iPhone set to use iCloud anyway, decided there I didn't need to also sync them when I do my iTunes sync.  After unchecking "Sync Books" and hitting "Apply" in iTunes, the every-time-I-do-an-iTunes-sync reminder to transfer purchased items have stopped.

Maybe when iTunes gets split up into separate apps (as I heard might/will happen) these iTunes sync issues will get sorted out.  But don't get your hopes up.  I think we're lucky Apple supports sync-to-your-computer-without-using-iCloud at all.

Other details: iPhone 7, iOS 12.2, MacOS Mojave 10.14.4, iTunes 12.9.4.94, Lightning cable.