You think this is topic drift? You haven't seen topic drift!
I'm seriously not being deliberately obtuse here (semiconscious, yes) but I'm not understanding what it is that you're doing that means you need to access your ebooks outside of calibre.
The need to keep duplicates of the files is simple: one set lives inside of calibre's "black box". Just imagine that it's a ginormous database and the files are being stored in some kind of ebook-specific BLOBs, and pretend they're not human-accessible at all.