Why I never use sync
This isn't a problem with iTunes, it's a problem with using "sync" functions at all. If I copy and paste files from one device to another, I know exactly what has been moved and where it's been moved to, as well as what might have happened to existing files with the same names and any other conflicts that might arise. If I use sync, all I know is that some things that were in one place might now be in another one. But I don't know what has actually been copied (all files, all new files, all files that don't already exist in the new location, etc.), where it actually is, or what might happen in various conflicts and edge cases. Worse, even if documentation is available, the software could be changed and start behaving differently at any time. A sync function could do exactly what you want for years, then suddenly delete all your local files one day because someone has decided that's how it should work instead.
The part I really don't understand is why anyone bothers in the first place. Syncing doesn't add any convenience. If I want to backup my phone, it's quicker and easier to just copy and paste all the files than it is to load up some badly written interface software, wait for it to actually find my phone and figure out what to do with it, and then carry out so unknown sync function that may or may not do what I expect but ultimately just boils down to copying and pasting anyway. If there was added convenience I would understand why it seems to be popular, but it seems people are happy to enjoy the added risk and uncertainty in exchange for also being less convenient. Weird.