Completion to #3.
Take a public domain EPUB, that was not touched by calibre.
(1) Convert to AZW3 through calibre. The result is with small fonts.
(2) Convert to AZW3 through kindlegen. The result is with normal fonts.
(3) Convert to MOBI and from MOBI to AZW3 through calibre. The same fonts as (1).
Here I used Calibre the environment.
(4) Convert to AZW3 through ebook-convert (command line tool). The result is with normal fonts.
Calibre the environment breaks the font sizes somewhere on the way.
How to fix this?
The more I play with these. the less I understand.