I am using Intel RAPL to measure energy usage of a system. On a motherboard, the fan is typically connected to the CPU for temperature control.
I think RAPL is internal to the CPU package / silicon chip itself, thus it has no idea about current going to other things outside it which might happen to be physically connected to it.
The CPU fan header on a typical mobo wouldn't even be pulling its 12V (PWM-controlled) supply from the special CPU-power connector; I think usually only the CPU voltage regulators are fed by that supply.