Why call this "defection"? I interpret "defection" as meaning not just "a bad thing people do" but as deliberately deviating from a previous agreement. The relationship between the prisoner's dilemma and not being sufficiently polite seems forced, or at least like it could have used more thorough explanation.

I wanted to put this into a context of how you could cooperate, raising everyone's payoffs - or defect, raising your payoff at the expense of the other person.

Which might be fine, if you do it consciously. But is really something you should be aware of. Certain kinds of public statements have this effect - raising your standing at the expense of who you're criticizing, like in the meeting example. This might be okay to do, but you really, really should be aware of it. A lot of smart people don't realize that their action/criticism comes across as defection - raising themselves at the expense of lowering the other person.

Second, lack of politeness is a countersignalling method to indicate friendship and community by showing you are close enough to a person that politeness is unnecessary

Yes, but I don't think this is what the majority of technical people are doing when they're going around accidentally offending people. Think of the I.T. Guy stereotype who constantly insults everyone else in the office for being so stupid, but is unaware of it. That's a stereotype, but there's a grain of truth in it. There's a huge difference between that and being loose and easy around your friends.