calibre does not compress files, it does not store all books in one file, it is perfectly possible to do differential backups with calibre's library (I do it all the time). You can change where calibre stores its books, in fact you can have multiple libraries at different locations. You can run calibre entirely off a USB key if you want to.
The OP really should ask about things before making assumptions and then complaining.
And I defy anyone to give me a single use case where having calibre support their pet folder structure is better.