To add chapter marks to a pre-existing Mobi file with a decent HTML table of contents already inside it, I'd say
- unpack using the Mobiunpack script
- copy-paste the TOC section and then
- regexp or otherwise search/replace the HTML bits surrounding the chapter titles and anchor links to create an NCX
- fill in the PlayOrder and other necessary pieces
- regenerate the Mobi, linking your new NCX
It's not exactly easy, but it takes marginally fewer steps than the Calibre to Sigil to Calibre/KindleGen round-trip.