I understand that you understand; I already knew that
It's just that with some programs I prefer a folder structure (as with FooBar, as I use only one music format), and with others I prefer a library structure (as with Calibre, as it needs to manage at least two formats: my base EPUB, and currently, AZW3 for the Kindle).
I think it's good that you actually can extract "normal" files from Calibre's library without using the program, if you ever need to for some reason. There are some backup programs for example, that stash your backup into a proprietary database, which you can only access using said program. I hate that. If you need that backup, who says you actually have that program available to read it? I'd never trust my data to a program that works in such a fashion.