@alikayn: If you were using a program (say Outlook) to organize Contacts, would you expect to see on your computer directories and files corresponding to each individual contact? No... you would be content in the understanding that you only access the contacts VIA Outlook.
If you use Quicken to manage financial transactions, would you expect to see files on your computer where you could access an individual payment? No... you would be content in the understanding that you only access the contacts VIA Quicken.
Calibre is no different; it is designed to allow you to access material from within it, via it's interfaces. The fact that it stores books in directories named after the author and book title is purely irrelevant. These structures are for ITs usage; not ours.
If we want to access material in calibre by our own means, then, as in either of the above examples, we need to export the material at which point we can organize it how WE want.