The music library app is especially tuned for ways to view my music that make sense for music. It makes those easily accessible. The file system is wholly inadequate for that task.
The library app takes care of the underlying folder structure – but that’s an implementation detail I absolutely do not care about. I don’t even know how it looks. (I just looked it up, it’s “Artist” – “Album”, the same structure I used before I started using a library app.)
I’m not sure that the file system is really so bad (at least I’m relatively comfortable with it) but I do think that for certain specialized tasks it’s massively preferable to have dedicated apps. Music and photos are my two prime examples.