I think some of you are missing the point here. They are using metacity, because it's the common denominator among all of the applications on the desktop. This way, they need only patch metacity, and not every single gtk/qt/wx application in existance to have an area that isn't necessarily a part of the application, *in* the application window.
It's a plugin system, so yes, sure, they can add functionality to the application in question as well. But i'm pretty sure this is not meant to remove buttons from the application in question just to put them in the window titlebar, but adding a sort of plugin system to some applications without patching/forking them too much. Perhaps, only light modifications (probably only some type of signaling system) are needed to the apps that will make significant use of this functionality, but that woulds also mean it should be backwards comaptible (if done right) with a normal (or vanilla gnome desktop if you will). So don't cry wolf just yet.
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