[pthwaite]

I'm not sure I understand your problem, however:
I use the Calibre newsfeeds adn set the defaults to Mobi and they succesfully get transferred to the DR, no issues. Yes they go to the ebooks, News... directory but that is hardly a hardship as it's easy to navigate the DR.
The newsfeeds generate a TOC at the end of the feed and tapping on any item in that takes you to the page. In my case I never use the TOC, but it does work. At least with the newsfeeds I use.

Additionally you can manually save your books, newsfeeds to whatever direcory you want, just use the save to disk function in Calibre and set it so it doesn't auto save to the DR.