My memory of the 747-200 AFM is that baseline rated TO performance is based on APU running, and that an APU OFF takeoff incurs a few hundred Kg TOGW penalty.
I was told by a Boeing flight ops guy that the APU actually generated a small bit of thrust, and that Boeing treated this as a 4.001 engine takeoff (as opposed to 4.000 engines). Don't know if this is still true.