They didn't have knowledge of the exercise. You give them way too much credit. They didn't have knowledge of white house codes either.
As for the codes and communications procedures, White House sources leaked that to Safire and others at the time to explain Bush's absence from the White House until the evening.
As for knowledge of the exercise, that could have been a coincidence, sure. But the prudent thing is to assume that it was not. In any case, I don't understand how you could have knowledge that it was just a coincidence. Care to explain?