Perhaps the electronics works it out? Maybe it starts up with both pulses then it would be easy to cut off one of the firing and injection pulses and see if the rpm drops. Once the electronics figures out which pulse dictates the squirt and the bang it can turn off every alternate one. Also there is a permanent live to the ecu so it would not need to figure it out on every start just when the battery had been disconnected. Weird though as that ecu family is used on other motorcycles and even some Fiat cars presumably with a cam sensor?