[Shane@DBPerformance]

Airflow. It is much harder to get perfect air distribution to 4 cylinders through a throttle body, plenum, runners, intake port, past the valves, in an environment that is always changing. Versus a straight tube in which the pressure delta should always be the same, unless the fuel pump can't keep up. Even regardless of airflow, temperature can cause one cylinder like #2 to be more prone to detonation, because it is sandwiched between 2 other hot cylinders. Often with a standalone system, you might give more fuel or less timing to the center cylinders. The 03-04 Supercharged Cobra has 2 cylinders on side of the motor that are most likely to go first because of the stock cooling system.