Could it be possible that the phone calls were a part of a drill like Amalgam Virgo 02?
"Before September 11, 2001: NORAD Plans a Mock Simultaneous Hijacking Threat from Inside the US NORAD plans for the Amalgam Virgo 2 exercise. The exercise, scheduled for June 2002, involves two simultaneous commercial aircraft hijackings. One, a Delta 757, with actual Delta pilots and actors posing as passengers, will fly from Salt Lake City, Utah, to Honolulu, Hawaii. It will be “hijacked” by FBI agents posing as terrorists. The other will be a DC-9 hijacked by Canadian police near Vancouver, British Columbia."
The phonecalls are obviously the 2001-equivalent of the Mayday-signal from Operation Northwoods. Doesn't it make sense that a standard element in a false flag would be part of a drill, as any major aspect of the operation seems to have been carried out under the camouflage of drills?
Perhaps the commercial planes landed on a base of some sort, which was then followed by a drill. Such a drill could include that passengers, recruited for this purpose, would make a few phone calls.
This could explain the calls given the near-impossibility of calls at the altitude of a commercial airliner, without necessarily resorting to explanations that would seem outlandish to the average person. In fact, it would probably mean that the calls were indeed placed by the people that they're attributed to.
It could also explain the fact that the planes were almost unoccupied, but that's another issue.
I don't have enough information at hand about the actual calls to judge this possibility, so if anyone could support or challenge it with details, I would be grateful.