Well, yes it does matter. Conventional ignition systems are designed to work best with a negative voltage to the spark plugs. This is because the negative voltage is the source of electrons. So, electrons will emit from a hot surface or object more efficiently and it's the tip of the spark plug that is hotter than the grounded side of the gap so the electrons will more readily jump off of the tip. That's the basis for the design of such exotic spark plugs as Iridium's or platinum tipped spark plugs. Those precious metals can get a lot hotter than a copper tip and so they emit electrons more readily but only if the voltage is negative.
The polarity of the voltage to the spark plugs is determined by the polarity of the primary. If you reverse the primary wires, then you will end up with a positive voltage to the plugs and they will be less efficient by as much as 40% meaning that the voltage has to be 40% higher to obtain the same efficiency.
Now, this begs the obvious question. What about a dual output coil? Yes, a dual output coil produces a positive voltage on one plug wire and a negative on the other, so the positive spark plug is less efficient and exotic spark plugs are a waste of money on the positive wire. That is why you will find most dual output coils are high performance "Flame Throwers" because they have to produce a higher voltage for the positive wire.
Virtually all modern cars use dual output coils and that is why they need that very high voltage. Ford recognizes this phenomena by specifying a different spark plug for each of the paired cylinders. One for the positive wire and one for the negative wire.