Ah, it appears "Saving books to Disk" is completely different feature entirely. It does not change the way Calibre "saves" or manages it's internal database folder structure.
I'm guessing it is not possible to change the way Calibre stores books in its own library database. I can only change how it saves "To disk" or "Sends to my device".
http://calibre-ebook.com/user_manual/faq.html#id29