Some folks panic if the output of the magneto/spark coil is not negative polarity on the spark plug center terminal. There are some theoretical advantages but in the real world it does not matter. There should be at least a 100 % overhead for a decent coil. In other words, if the plug needs 10k volts to initiate a spark then the coil should be able to produce 20k volts. Switching the polarity will increase the needed voltage to initiate a spark to around 30% so that 10k volts becomes 13k volts but the coil can still produce 20k volts, much more than is needed.
As barry ayres stated, most magnetos switch polarity each 180 degrees of rotor rotation. Some, the Wico EK as an example and some single cylinder rotary magnetos, do not switch polarity. However, you have to polarize the magneto magnets somehow so for the uni polar magnetos, Wico EK etc.., you might as well polarize the magnets correctly.