This is all true, but you can come up with situations where exchanging source code is more relevant. For instance, Robin Hanson has frequently argued that agents will diverge from each other as they explore the universe, and that someone will start burning the cosmic commons. This is a Prisoner's Dilemma without traditional communication (since signals are limited by lightspeed, it would be too late to stop someone distant from defecting once you see they've started). But the "exchange of source code" kind of coordination is more feasible.

Also, I don't know whether anyone polled traditional game theorists, but I'd bet that some of them would have expected it to be impossible, even with exchange of source codes, to achieve anything better than what CliqueBot does.