Let's be a bit cautious here: there are some cases when developers would accidentally leave out certain things that was supposed to be corrected, but was left untouched at the final release.
And here's one problem: the Belkan Air Force emblem and black paint can be considered as a big military no-no in real-life. They would have been caught and the war (including the Grey Men's plans) would have ended much quickly, assuming that those loyal to Nikanor would have gotten hold of the radio signals and flight recorders.
Also, how it got there: you have a country that is almost as large as Canada and, judging by the situation prior to White Noise, Yuktobaian radar and aircraft have a pretty decent chance of detecting it at the time. Of course, they could fake their allegiance but you have to fly at a pretty low altitude and/or get hold of some electronic warfare equipment and reconfigure the E-767 to both jam foreign communications and radars, and maintain communication with the Belkan operatives.