The boot-args are in addition to whatever is in the plist. If you don't want one, just set it using nvram boot-args="-v other flags" or delete it with nvram -d boot-args. Alternatively you can update the boot args in chameleon by updating the command line.
I get what you're saying but most people are used to updating boot args by editing org.chameleon.boot.plist. This module changes that process and it would be good if the module obeyed what has always been the way to set boot parameters instead of forcing users to learn a new way.
If its technically not possible based on the chameleon module architecture then that's one thing but if possible, it would be good to have the option. You could always open source the module and let other developers add that capability ;-)