I apologize if we sound harsh -- in the past, people have complained, whined and trolled about the file structure of the library backend, to the point where it has become a sore topic.
There is an official sticky and an official FAQ entry as a result, and Kovid Goyal has made it clear that every objection raised will not change his mind -- it is simply not worth it to him to change the library structure at all.
There are several approaches to dealing with the matter, including just dealing with it. Or duplicating your library using save-to-disk.
theducks is merely pointing out that
if you simply cannot live without calibre keeping its hands off your carefully chosen filenames... then perhaps calibre is simply not the tool you need.
And the one and only person in charge most emphatically will not change calibre's direction and make it that tool either.
Use the bits of calibre that you like, and get used to or reject the rest. You wouldn't be the only person to write custom scripts utilizing calibre's rich CLI backend to do things strictly the way you are used to.
Good luck, whatever you decide.