The article says there are two ways - the pilot and the airline. However if it was the airline, that would be quite a big conspiracy - saying that the airline wanted to divert its own plane. And ... if that sort of thing happened, with the pilot not being “in on it” - then he would take control and override the control.
In this case, you can be assured it came from the cockpit and that it was someone who knew very well how to handle the equipment.