I just read this too a couple hours ago... but some parts confuse me, and I'm sure it has to do with the normal misreporting of aviation stuff by clueless reporters. For example,
"By late 2001, he was the only pilot from his training class who had not made captain. Reported incidents included once lining up at the wrong runway."
The article makes it sound like that guy did the actual taxiing when technically, only the captain can taxi the plane. I would think if the crew did line up for the wrong runway, it would be collectively their fault, not just the FO's.
Also,
"Khan passed two of those portions after retraining, but during a third placed his aircraft into a dive. The supervisor took the controls to prevent a crash."
Obviously, this "retraining" and the PC must have been done in a sim... and that is only obvious to me because I'm a pilot.. but who actually takes over the controls to "prevent a crash" in a SIM???????????????? Can we say dramatized and inaccurate?! If I heard that as a non-pilot, I would think it happened in an actual airplane as there is no mention of a sim whatsoever.
As far as the "dive," I dunno what actually happened with this guy, but one of the few things I can think of is maybe he had a V1 cut, autocoarsen failed and he didnt act fast enough? My sim partner and I both dived/crashed the sim during that scenario in one of our first abnormal sims, but our instructor didnt rush to "take over the controls to prevent a crash".. all we got was an ominous red screen, and besides I think he actually wanted us to see what would happen by making the mistake we did. Granted, someone going through a PC shouldnt be making the same mistake.