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.
The trick was to skip the onboarding and go into the Preferences, there was an option there to disable putting your files in the music library folder and messing with the layout
edit: I just compared iTunes 4 and Music in Tahoe and they still have the same preference! It's funny how they clearly did a s/iTunes/Music/, resulting in the "Music/Music" dir https://kalleboo.com/linked/itunes4-vs-musictahoe.png