While these are all possible threats, the question is, how probable are they? Resource expenditure on security threats just because they are possible means that those same resources cannot be spent on those far more probable. Moreover, if there were full implementation of the program to permit pilots to be armed, the more probable threats would become less so. In other words, arming pilots and some crew members would lessen a whole class of security threats.
The TSA's determined opposition to passenger profiling is in itself a threat to airport security. Take their additional screening. They have every incentive to be politically correct. But suppose the TSA had to pay $1,000 to each passenger they selected for additional screening who was found to be no security threat. You can bet they'd develop a screening method that made more sense, and it would include some sort of passenger profiling, including racial profiling. And, by the way, liberals shouldn't fret, because the U.S. Supreme Court has ruled in several affirmative action cases that provided there's a compelling state interest, race can be used in decision making.
It's my opinion that sensible TSA security measures would allow us to reallocate resources away from policing against possible but improbable threats to policing the far more probable source of threats -- one being our border with Mexico.