I think the core lesson of the story is knowing if your hobby is listening to music or curating a music collection. Optimize for one or the other.

I went from meticulously curated MP3 collection on Linux to letting iTunes do it for me, and I realized that the meticulous curation and hunting down album art and everything was a hobby I didn't actually love. But if you do love it, great! Different tools for different jobs.

I remember the trick was to use a network hard disk or drive for the music. iTunes kept the organized folders and all files untouched while building its metadata-only archive in local. But in general, yes, the tendency to mess with your file was built-in.