I suspect that many of those complaining have never written software. Treat the internal representation of the files as a black box and you're fine... the layout on disk is an implementation detail, likely to change at any moment.
As others have said, you're free to write your own library management user interface on top of the existing ebook-convert tool and have it put the files wherever you want.
I personally use Calibre only from the command line. I find that Calibre doesn't work for me, only because I don't need its vast feature set, I merely want to convert books from various formats to read on my Kindle, the management of them I do manually. The fact that the developers split out the backend functionality from the GUI means that I have the flexibility to do this, and you do too...
Learn some Python, learn some Qt, download PyQt4, and write your own interface that does whatever you want it to do using the calibre backend to the do the actual work, and be happy that somebody already did the heavy lifting for you.
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