Good points, Dave!
I wonder what the solution is? Government agencies already have logo policies that try to limit the brand-within-a-brand problem. Agencies also have some scary sounding penalties for straying from the brand straight-and-narrow.
Is it that we need something that’s more user friendly? The Twitter logo guidelines strike me as an especially clear and well-done example of an organization trying to do away with alternative logos that are confusing, if not competing.
But the essential problem remains: How do you tell some important guy that he can’t have a special logo for his special project?