mkqnximage doesn't add every file anyone could conceivably want. Instead it provides a base set and ways of extending it
.

If you build an image you'll find you have a file local/snippets/system_files.custom. Anything you put in here will get 
merged with the build file used for generating the system partition. So all you need do is add lines to include files 
you want. The format is as used my mkqnx6fsimg since this is the utility that ultimately consumes the stuff. You can 
look at the build file that mkqnximage created, output/build/system.build to get a better idea of what goes here.

The documentation lists the other snippet files you can have.