The bitmask used by GetIRGPIO(and likely others) determines which bits in the GPIO registers to access. The output value from GetIRGPIO uses the same format as the bitmask: the values of bits in the output field are set to the value of GPIO data when those bits are set in the input bitmask.
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The bitmask used by the service commands determines which bits in the GPIO registers to access. The output value from [[GPIO:GetGPIOData|GetGPIOData]] uses the same format as the bitmask: the values of bits in the output field are set to the value of GPIO data when those bits are set in the input bitmask.