A coil will not set a knock sensor fault in this vehicle. Knock sensor faults are set when the vehicle is running extremely lean to the point of detonation setting a "knock" causing the ecu to retard timing. The most likely cause of your vehicle setting a knock sensor fault and not passing emissions "most likely due to high NOx" is a stretched timing belt, you will need to have your timing belt replaced soon to prevent serious engine damage.
Possibly, but they probably communicated, they will fail you if there are any emissions related fault codes such as misfires, knock sensor, O2 sensor ect. You probably also had high levels of NOx gas coming from the tailpipe as well.