You probably are right. If the secondary winding have to leads, let's call them A and B. Say that the voltage generated in it is 20.000 volts and that lead B is connected to ground. Then, the voltage in lead A - voltage in lead B is 20.000 volts (VAB=20.000)
Say that we put lead B connected to ground. Then, Va=20.000 volts. If we connect the A lead to the spark plug, we should have 20.000 volts in the inner of the plug above the spark plug body, so there would be spark. Both plugs should be connected to lead A.
Now if we connect lead A to one of the plugs and lead B to the other, if we measure between ground and lead A we will see +10.000 volts, and measuring between ground and lead B we will see -10.000 volts. That way, Va-Vb= +10.000 - (-10.000)=20.000 volts.
In one of the plugs the current flows from the live inner electrode to the plug body, and opposite in the other spark plug. That could be the reason why they recommended to swap the plug caps.
In that case, it would be true (and if you say so it is) that if you remove one of the plugs the other will not spark.
Regards
Raul