I understand why GNOME is choosing the technical measures it is making to try to make the distinction. I have nothing to comment on the technical measures GNOME is using to delineate a space between extension and the base.
But I continue to be baffled by where the line in the sand is in regard to allowable downstream customization. How much downstream changes in default UI is too much and still be GNOME? It's never been clear in the 2.x timeframe and I'm still not seeing clarity for 3.x. That lack of clarity is in direct conflict with assumptions you want to make about distributor actions. Without clarity as to what you expect distributors to refrain from doing, they will wander out of bounds again and again without meaning to act in bad faith. Because well, you haven't defined the boundaries of what good faith action is.
I'm not suggesting that you _have_ to pull out the trademark enforcement big stick. But you need some form of clear guidance. You don't even have a compliance test suite or a standing set of "thou shall not" commandments...bright line tests of any sort...which define the narrow path of correct action with regard to what is expected of a downstream vendor who wants to label the deliverable GNOME.