The reality of things was that the guild was always under government control. In fact, the guild itself was a creation of the government and was being funded as well as managed by them too. These things were not known by anyone other than those that were at the highest chain of command at the guild. That was why the guild looked to be a neutral party that merely worked alongside the government at times.
It was done in a fashion that would draw a line between the government's armed forces, army, navy, and in very rare cases their air force. This was a world of magic and flight why not a common thing was something that still existed in various forces. While not everyone was capable of flight on their own or assisted. There were still various mounts and other creatures that existed in the world that were capable of doing it themselves.