Instapaper has apparently solved this issue. It can deliver periodical-formatted documents via Amazon to the Kindle Touch. Does anyone (esp Kovid) know what the magic fix is? I am the developer behind Kindlefeeder and also the open-source kindlerb ebook generation tool.
My tools can make MOBI documents that display the periodical-style table of contents and navigation when you transfer the files manually to the Kindle Touch or download them through the Kindle Touch web browser. But if you email these same MOBI files to your Kindle Touch via the @kindle.com wireless delivery service, the peroidical formatting goes away and the MOBI ebook reverts to regular ebook navigation.