I am sorry, this message may be better sent directly to shazron, but I thought others might be interested too.
I just built up a new Cordova 3.1.0 project, installed the device, console, splash screen, testflight and my own plugin. They all installed in a way that I did not have to add any script include tags in my html - they are part of the cordova_plugins.js. All except the test flight plugin. That one I had to add the plugins/testflight.js. Perhaps shazron can add the magic to the plugin.xml needed to get it installed automatically? Looks to me through a simple compare it is the js-module element that is needed (it has the clobbers element that is in the cordova_plugins.js file. The plugin is working great besides that little niggle BTW. Thanks, Tyler