Hi Peter
I’m guessing here, but if I were using a DSLR, I would use the same ISO for lights, darks and flats. If the ISO “value” is a property of some on board circuitry processing/software algorithm, then I would try to ensure that all the incoming data, whether lights, darks or flats, are subjected to the same processing.
Therefore, I would vary the exposure time. However, I could be wrong!
Cheers
Dennis