Its how the coil/transformer is wired internally. There is about a 30% difference in voltage.
This isn't quite true, the voltage output from the coil will be the same magnitude either way, but its direction will be different.
The secondary winding in the coil has one end leading to the high-tension terminal that goes to the plugs. The other end connects to one of the low-voltage terminals. That's how it makes a circuit. If the coil is wired up in such a way that the reversal of the magnetic field (caused by the opening of the points) creates a voltage in the secondary winding that pushes electrons
toward the spark plugs, so that the current in the plug flows
from the center electrode
to the side electrode, the resistance of that air gap is relatively lower.
If the coil is wired up the other way, so that the voltage in the secondary winding pushes electrons back toward the battery, thus in effect "pulling" electrons from the ground electrode across the gap to the center electrode, the resistance of the air gap is relatively higher.
If the resistance in a circuit goes up, and the voltage stays the same, the current goes down. Since the coil is a transformer that
always generates the same voltage (assuming constant performance of the points, condenser, battery, etc.) if the resistance of the spark plug air gap goes up, the current crossing that gap, i.e. the strength of the spark, goes down.
As the engine runs faster and hotter, the resistance of the air gap goes up independently of the coil, because the air between the electrodes is being dispersed by turbulence as the plasma arc tries to form. So the practical effect of the coil wiring not matching the plug is that, at any given rpm and load, the strength of the spark will be weaker, and at some point the spark will simply stop.
So it would be more accurate to say that, if the polarity of current in the secondary winding doesn't align with the spark plug, the spark is 30% (or some number around there) weaker. It may also be shorter-duration; I'm not sure, this is roughly where my electrical understanding runs out.