MOBI files contain a compiled version of toc.ncx that ebook-convert will not convert. The toc.ncx generated by ebook-convert is from the embedded TOC in the MOBI file, which is just a flat list of normal HTML links. Presumably Instapaper doesn't generate the embedded HTML toc.
In any case that is irrelevant, as the embedded HTML toc is not used by the Kindle for periodicals. Try generating a calibre periodical for a news source with only one section to compare with the Instapaper one.