I wrote up a thing on how to use it on the Mac in
post #362 upthread.
When using the .pyw GUI, double-click to open the app instead of dragging and dropping, and check the split option in the dialogue box, and that IIRC should give you a .mobi7, a .mobi8, and a kindlegensrc.zip output.
For using from the command line, you want the -s option.
It's possible that it auto-splits and also extracts the Mobi files (been a while since I bothered to use it, as I only have a K2 and use an older version of KindleGen which creates Mobi-only), but you can ignore those pieces and only bother keeping whichever version of the .mobiX you need.
If it still seems bloated afterwards, you can run Kindlestrip on it to make sure the source files are no longer there.