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You do understand, don't you, that Calibre doesn't touch the layout of your books? It makes copies of them, and sets them up with a name and directory structure that you should never, ever, ever, need to look at. As others have said, Calibre's copy of your books and the directory structure it uses should be treated as a black box. When you want a copy of your books, you can have them with any name and in any named directory structure you want. That's completely configurable. It's the behind-the-scenes do-not-touch-or-look-at system that can't be changed.
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Heh, yea I realized this a bit late. In my case, I actually deleted the copies and am now backing up my user-edited authors. I will be trying to bulk-download meta data and see how it works out. If it screws things up, I always have my own backup copy.
I read a lot and have over 490 books (mostly free books from Mises.org.
And for those of you who don't know, Calibre works perfectly in Sandboxie (a sandboxing program). It prevents me from having to backup/restore settings (royal PITA, IMO) when I reinstall windows.