I think that's just if you wanted a PWM controller. The pumps are setup with a PWM plug with the blue/green wires AND a standard 12V Molex plug. You should be able to control this fine with a MB header from what I've gathered. The molex feeds the power and the 4pin fan header plug does the speed control work. No yellow/black on the fan header, those are left empty.
Here is a picture skinnee posted earlier on the rad/res/pump kit which shows the wires/plugs:
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