The sonic boom isn't created when the aircraft transitions through the speed of sound. Although I never hear it explained this way, I believe it is caused when the velocity of the aircraft with respect to the listener transitions the speed of sound. That's when the sound waves approaching the listener bunch up and cause the boom.

When the aircraft is directly above a listener on the ground, the relative velocity is zero, so you can see how the velocity changes from greater-than-sound to less-than-sound (twice) as the aircraft is approaching and then departing with respect to the listener. Thus the listener hears 2 booms.

The boom is usually explained in terms of shock waves emanating from the aircraft, but I think my description explains the phenomenon just as well, but more intuitively.