Back whenever iTunes was first made available for Windows, I got it, imported my music collection, and watched iTunes completely screw up track names, files and folders. A later version (or at least discovered later by me) had a checkbox for NOT allowing iTunes to "keep my collection organized", which is the only thing that made it usable for me. So even in Steve Jobs days, iTunes could screw up your music. This problem isn't occurring for the first time, and it probably won't be the last. As I see it there are two factors at play:
1. Music identification is actually somewhat of a hard problem. Identical tracks can belong to more than one album, and if you are into rare recordings or local artists, it is worse than useless. The classical music market has lately been driven by compilation albums, which means that any normal album you import may fragment into several compilation labels. How many third party apps are there that claim to fix your iTunes? Some apps other than iTunes do better or worse at this. The only solution is to add items slowly and make corrections manually, and then NEVER allow an app to change information. As a result, I have multiple apps that I use to access my music, but none of them get to change files or folders, except a tagging app when I want it to.
2. It is in Apple's DNA to control the user experience more than most in order to make things "just work" for most users. This is often a good thing, and one of the benefits of tightly controlling hardware and software integration. It causes headaches in other areas (not being able to get apps approved, etc.). The control of music probably works well for the average user, and is a headache for audiophiles with unusual collections. There is a dance that Apple does: release a tightly controlled experience, and then make options available to give up some of that control for users that have different needs or know what they are doing. Eventually, they find the sweet spot in the Larry Wall Philosophy: "Easy things should be easy, and hard things should be possible". Apple has made two mistakes with Maps and Music, and they are based on the same problem: You cannot develop a service overnight, and expect it to be as usable as a service that has matured over time with many user interactions, issues and bug reports.
I've been doing some testing of Apple Music, Spotify, Pandora, Google Play Music, etc. Apple Music, even without the issues on this thread, was simply confusing to me in what it did with the UI on devices and iTunes. When I started playing with Spotify, I thought "Oh so THAT is what they are trying to do". I may keep whatever free options are available for all of the above (which are similar, except for Pandora), but I finally went for the paid option with Spotify, because:
1. Spotify is easy to use and understand, and makes sense out of the box. It also will play or sync local files without touching them, but in 80-90% of cases, it already has the music I have and more. That is only a slight edge over the other services that are similar.
2. Spotify is now integrated into the djay app on iPad. That was the kicker for me that pushed me over the edge. Other services will probably be integrated into DJ apps eventually, but right now, Spotify has it, and that was more valuable than a bunch of other features.