Thanks for the replies. I just remembered why I was using kindlegen in terminal instead of ebook-convert: kindlegen doesn't mess with the negative margins that I set in the epub. Calibre seems to zero it.
I set negative margins using EbokJunkie's script here:
https://www.mobileread.com/forums/sho...4&postcount=27 (thanks EbokJunkie)
Negative margins because I find the default paperwhite margins too large.