The
long explanation of why we aren't allowed to alter the directory structure of Calibre begins with pointing out the disadvantages of storing metadata in the filesystem.
But Calibre stores metadata - specifically the author and title - in the filesystem. In two places each. The author happens to be one of the specific things that the aforementioned long explanation cites as problematic.
If Calibre could refrain from doing this, it would also be more compatible with other software that has its own requirements for filesystem use. Such as Nook, which is useful for downloading files from
Barnes & Noble but cannot handle subdirectories and gets confused if the name of one of its files - which includes a catalog number - is changed.