The files get hardlinked and the folders are created as needed -- I find it simpler to rename the folder, just like you.
There is a good reason to let calibre handle author-book folders -- it needs to, in order to get them right, the OS has no ability to handle that properly.
Besides, calibre leaves behind anything it doesn't index, occasionally there can be meaningful things there, for one, the Dropbox index. The OS does things the way I tell it to.
