EEC-IV, I believe, had the capability of doing a power balance test during the KOER test. Not sure if OBD-II (EEC-V) has this capability.
In any event, a cylinder power balance test involves shorting the secondary ignition to ground, not primary. This does not involve providing an open in the secondary circuit (e.g., pulling off a spark plug wire to disable a cylinder). You are in essence allowing spark to go directly from the coil tower to ground instead of allowing the spark to jump across the spark plug gap to ground. This is no way damages the coil, ignition drivers (transisters), computer, etc.
Damage could be caused, however, if a person were to pull a spark wire from the plug to disable a cylinder since the spark will find its own path to ground, possibly through the coil and or/drivers.
As far as the test not being applicable to waste-spark ignition systems, that is simply not true. The secondary circuit is never opened during the test. The spark only bypasses the spark plug gap on the cylinder being tested, thus not allowing power to be produced on that particular cylinder only. The companion cylinder spark plug fires normally on both the exhaust and power strokes.
Sorry about the long post, but this is an extremely useful and powerful diagnostic tool that has many misconceptions.
