Interesting! This is pretty nifty.
One thought: wondering if the option to display widget areas "manually with PHP" fits with the purpose of the plugin? If they can add the PHP to display the widget in the theme, they can also add PHP to register the widget area as well. But I suppose it has the benefit of not having to manually write out the widget registration code, and keeping widget area registration portable from theme to theme.
No big deal, just a thought.
Again, really cool plugin!