Must... resist... urge... to... lecture...
Repeat after me. "The Calibre library directory is not a file structure. It's a database." Repeat one hundred times or until you've convinced yourself.
The point is that you shouldn't ever peek under the hood. Calibre has a reason for organizing files the way it does, and you shouldn't be questioning it any more than you should question why the engine of your car is set up in a particular way. Sure, if you know what you're doing and you're extremely careful, you can work with the files in the database, just like you can tune the engine of your car. But doing so should never be a part of your regular work flow; it should only happen in extraordinary cases. If you're working at that level, you don't complain about how you wish things were set up differently; you accept that you're dealing with someone else's decisions about things you shouldn't even be looking at in the first place.
Sorry about the rant. Now I'll try to be helpful.
The first question you should ask is how to do what you want to do WITHOUT PEEKING UNDER THE HOOD.
This will naturally lead to another question: why do you want to use Calibre at all?
More specifically, what features of Calibre are necessary for what you do? If you prefer a particular directory format, why not just store your books that way and bypass Calibre completely?
If you like Calibre's reader, you can always associate ebook files with the reader and open them by double-clicking them.
If you want to use Calibre to convert ebooks to your favorite format without using the library management features, just set up Calibre with an empty library. To convert a book, drag and drop into Calibre, convert, save to disk, then delete from Calibre.
If you want to access your books remotely, use the Content Server.
But if you like Calibre's library management features, then only access your books through Calibre. In special cases where Calibre is not available on the platform where you're working, you have two choices:
1. Use a Save-To-Disk template to export the library to whatever structure you want.
2. Go ahead and peek under the hood, but understand that it was not designed for this. When you lift the hood of your car, you assume responsibility for anything you change. Likewise, when you access Calibre's library directly, you are assuming the risk for what you do. And in both cases, you don't complain when things aren't set up the way you want.
I would recommend against the latter option, but if you're very careful to look but not touch, there's no reason it shouldn't work.