I'm wondering if ebook-convert can generate mobi files with TOC like that made by kindlegen. Here are some screenshots of the two mobi files converted from the same epub by ebook-convert and kindlegen respectively.
ebook-convert:
https://i.imgur.com/rlJeoIp.png
https://i.imgur.com/ItjHEK7.png
kindlegen:
https://i.imgur.com/bGFXPlA.png
https://i.imgur.com/1eq3xQw.png
Sometimes I like the TOC made by kindlegen as it allows me to turn to the conver page. Besides, kindle can display covers on the kindle library.
But files converted by calibre ebook-convert can only show titles without cover images.