kindlegen is creating a dual-MOBI.
I assume you mean it is bigger than a dual-MOBI that calibre creates. (Rather than being bigger than a standalone AZW3 which is just duh.

)
Try using the undocumented
Code:
-dont_append_source
switch to kindlegen -- by default it creates a MOBI that has both mobi7 && KF8... and also the original source files, because reasons.

For kindlegen.ini that would be the "donotaddsource =
False True" mentioned in the OP.
...
Also consider creating the standalone AZW3 and MOBI, and sideloading each one as and when needed.
Unless you intend to use Amazon PDOCs of course.