I would venture to say the best way to get control is to designate how it should look in the source EPUB. Then allow kindlegen to receive its instructions from there
rather than letting calibre kludge it into shape. If only because KDP apparently doesn't accept dual-MOBI unless it is from kindlegen/previewer, and doesn't accept AZW3 period (all those old devices can't read it). And only uploading MOBI means new devices don't benefit from AZW3.
Create a dual-MOBI to sell through KDP with kindlegen, and upload calibre-converted files for your website.
Anyway... I converted the EPUB with kindlegen, sideloaded the resulting dual-MOBI to my Kindle Touch, and saw a ToC.
I don't care what Kindle Previewer says (I will never know until they port it to linux anyway), but it is wrong.
