I've found out by chance that Amazon has added a new KindleGen parameter that will prevent KindleGen from adding the source files:
-dont_append_source
I've only tested this with the latest Windows version (V2.9 build 0731-890adc2), though.
When this parameter is specified, KindleGen will display the following message:
Code:
Info:I9018:option: -donotaddsource: Source files will not be added