The sparkplugs for 1 and 4 spark at the same time, but only one of those cylinders will have gas/air/compression. The other cylinder will be on the exhaust stroke. Then 360 crank degrees later, the cylinders will reverse roles.
Obviously, the same will happen to the 2,3 pair of cylinders, but 2,3 are 180 crank degrees apart from 1,4.
So, it doesn't matter which plug wire goes to which cylinder, as long as they are going to the correct pair of cylinders.
Because only one of the cylinders in the pair is under compression when the spark happens, the spark coil only sees the equivalent of one spark plug. The cylinder on the exhaust stroke is at low pressure, so it's spark gap has relatively low resistance. So even though it seems wasteful to have a spark firing for no reason, not much spark energy is wasted on the exhaust cylinder, and the ignition system is simpler from a mechanical standpoint.
This type of ignition is called a "waste-spark" system.
