I have always understood that one of the benefits of Calibre (and the
recommended use pattern) was to ignore any file and directory naming and rely on Calibre's metadata. Let Calibre manager the underlying folder and file structure and don't mess with it.
If you export books to put on other devices, then you can export with whatever file and folder names you want as allowed by the destination.
You might want to consider moving this thread to the
Calibre forum section.