I was also resistant to not having full control over the directory structure BUT when you consider the size of hard drives today and how important our book collections are to most of us, it only makes sense to make full use of calibre's features. This includes keeping a "no touch except through the program" attitude to the directory structure of the library.
We can maintain our collections, add to them, and view them through calibre and for those who are as ocd as I am, do a save to disk in our own naming format.
Having two copies of every book is just normal backup for me anyway.
The only complaint I have is not being able to add a book in another format to an existing entry. Or maybe I still need to find how to do that
