Creative Speculation

... with a direct feed from the altimeter, and of course it's connected to power and the antenna. I wouldn't call those "systems" but there's no point in quibbling over semantics since the inarguable point is that those feeds do not provide any way to disable the squawk response, as you imagine. No, there is no software in a transponder. To do what you are claiming would require completely replacing the transponders with gimmicked boxes. But hey, I guess that's no big deal if you've already convinced yourself that it's plausible that the perps cooked up such a ridiculously complicated and risky scheme of fake hijackings and controlled demolitions, when something far simpler and less risky (e.g. a few truck bombs) would have accomplished the same presumed purpose. When you propose something that implausible, you need something resembling evidence, and your personal incredulity isn't evidence.