According to the schematic, this two pin is connected to the 5v directly and can’t be controlled.
I tried to spot the fan header in the design schematics and i think it is on sheet 21 labeled “U25” there. That would mean, the fan header is in fact not regulated and the 5V GPIO deliver the same flat power. The fan header is a JST PH 2.0 2 pin 2 mm, i think.