I also use itunes. My understanding is that it keeps own internal database of your music and its tags. It loads the database with information when you ‘add folder’, ‘add files’ or purchase from the online music store
summary answer to the first part of you question about syncing is no.
My approach is to keep my music in a folder on my hard drives with sub folders for artists etc. I edit the tags and info etc there using Picard etc.
To import into itunes, i delete everything in itunes and then add the top folder on the hard drive above. Itunes then recurses through and adds the songs using the tags and artwork in the files.
You can add or edit the metadata in itunes, but I’ve not seen it update back to the original files. Have you?
Also note that itunes provides access to only a subset of the tags available in the ID3 2.x ‘standard’ used for Mp3s. ( I assume you are using Mp3s). Also note that MB and Picard support all the ID3 tags and more. If you want that level of tagging in your files, editing in itunes wont allow it. My use of itunes is only to load onto my phone. I edit elsewhere.
I’ve also started using apps to play music other than the built in Music app which give better ways to sort you music etc. If you want to use Flac, there are some flac players available in the app store. so far I haven’t found one I like and that support carplay.
Regarding your problems with exclamation ! marks. I don’t understand. Can you explain more?