[DMSmillie]

There are two types of "Table of Contents". In EPUB books, and in most EPUB readers, the NCX file is used to display a table of contents to the user. In MOBI books on the Kindle, the NCX file simply enables navigation to the previous/next navigation point using the 5-way control button - to display a table of contents to the Kindle user, it has to be coded as part of the HTML content, with a Guide item entry pointing to it in the OPF file. An inline TOC is the only kind that can be displayed to a Kindle user.

So when you use Kindlegen to convert an EPUB file to a MOBI file, it isn't actually "losing" the table of contents - the NCX file remains part of the ebook - it's just that MOBI files, and the Kindle, operate slightly differently compared to EPUB files and EPUB readers.

Edit to add: What Calibre is doing is creating an inline TOC from the headings in the HTML content, adding that to the end of the HTML content, and adding the appropriate Guide item in the OPF file to enable the Kindle to link to the inline TOC in its "Go To..." menu.