I understand your frustration. The first couple of times I tried Calibre, I hated the interface. Then I started playing around with it and suddenly something just clicked, and now it just makes so much sense.
Funnily enough, what I hated about it was that it was too Itunes-like. I've spent decades getting used to a hierarchical file structure for organizing things. The database paradigm is very different.
As to your claim that Calibre is for programmers, it comes down to flexibility vs. simplicity. Calibre is far more flexible than Itunes, which admittedly means it sacrifices a certain degree of simplicity. But the great thing is that the hardest part is setting up the database the way you want, which you only have to do once. Once you get over that hurdle, managing your ebooks is a breeze, and far easier to deal with than Itunes.
Now, back to your original question. You have yet to clearly outline your problem. Calibre does not change file names on conversion, and it stores the author and book name in different fields. So your original statement of the problem is ambiguous, which is why you got several different answers, none of which solved your problem.
Which of the following is the issue you're having:
1. When you import a book into the Calibre library, you don't like how it interprets the authors and file names.
2. You're looking inside the Calibre library folder on the hard drive and you don't like the way it organizes the files.
3. When you use Calibre to transfer a book to your e-book reader, you don't like how it sets the authors and file names.
4. When you save a book from the Calibre library to your hard drive, you don't like how it sets the authors and file names.
5. (Something I haven't thought of)
All of these are valid interpretations of your original question, and all of them have different solutions. You can change the behavior of Calibre in all cases above except for the internal directory structure of Calibre's library (#2 above), which you should not be peeking at or touching anyway. The only way you should ever interact with the Calibre library is through Calibre itself.
If you will identify which of the above cases is what you're talking about, we'll be happy to give you a clear step-by-step way to solve the problem.