Sorry for butting in but I really don't see what all the fuss is about?!?!?
If you don't like to use calibre's structure don't use it! That's why it copies the files you add to its own structure.
I prefer to use my own structure so that's what I use, but I still find calibre very usefull because now I don't have to use a multitude of diferent programs to convert from one format to another.
I would love to have calibre use my prefered structure but as I don't code to save my life I'm just happy to have a problem which solves part of the hassle.