When playing around with the plist, I saw the different video plist strings affect the system by moving them to the /Extra folder. So, the plist in the live part is the one that is honoured, not the plist in the first hdd that originally starts Chameleon.
I think we're talking about the same thing using different words. Keep in mind that Chameleon also gives you the luxury (http://forum.voodooprojects.org/index.php/topic,351.0.html) to explicitly specify which com.apple.Boot.plist file to use:
Additional useful command-line options:
config=<file> Use an alternate Boot.plist file.
Edit: hotlinked the Documentation topic