Without being able to give a definitive answer, I would imagine it had todo with the transit and overflight gareements between the allies/NATO nations. Military aircraft in transit would not be subject to civil licensing or registration requirements, nor have to have commercial insurance, and would be able to carry armed and uniformed troops etc.
I would have got around the sort of problems that require those going to the Falklands to be in civilian clothing etc in case of a diversion to Rio etc.