Ok, so I took a look at my diagram and mine can use the 2 prong or 3 prong flasher. Now, with a 3 prong flasher, the indicator on the switch is fed from the third prong. If one of your external bulbs burns out, you will notice an immediate change in speed or failure to flash at all. This tells you that you have a problem.
With the two prong flasher, the indicator bulb is in parallel with the turning lights and if one of the turning bulbs burns out, you may not notice any change in the flashing rate. That would be my guess as to why the three prong is preferred.