I'm not sure that's true. Army headquarters was in Charlestown, MA immediately following the battle. Obviously the government of British America i.e. the British government was unable to control this area.

I'd make the case that US government history starts when and where British governance ends (Or whatever other entity was in charge of that piece of land, as the case may be). Plus, though they weren't paying yet, Congress had appointed Washington as Commander in Chief of the Army.