If we truly had plane swaps (which I believe we did) and some of the original flights continued on - such as the phantom radar tracks suggests for Flight 77 out west - then the "all flights land ASAP at any available base" certainly provided perfect cover for that.

Skpetics would argue that a 757 flying rogue across the U.S. would draw air traffic controller attention, but I think we can assume that once the "mandatory landing" order went out and every airborne plane had to ditch, there was no way all flights would be monitored as to where they came from or where they landed. They would have their hands full just organizing the air traffic around airports. And with all that going on, no one would worry about any planes making unusual maneuvers or devating from flight plans, it was probably close to total mayhem.

It's the perfect cover, because it serves the purpose to allow the disposal of evidence, plus it make sense from a standpoint of what could be seen as "normal emergency procedure." Just like Cheney's wargames were cover for the alleged hijackings, the flight grounding order may have covered up the real Flight 77's removal.