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I am not sure that is correct Colin. ISO is simply amp gain before the ADC. Higher ISO should not make the unevenness of the illumination any worse. That comes from the optics and sensor and dust. So far as I know ISO does not affect the unevenness of the illumination although higher ISO does reduce dynamic range. Most Deep Sky objects though have low dynamic range compared to a terrestrial shot with bright sun and shadows in the same image.
Flats are merely a shot of the unevenness of the illumination across the field from optics and sensor and removal of dust artifacts. So I am not sure why higher ISO would affect that as long as Humi says a decent histogram exposure is done (otherwise your flat would over/under correct).
Darks may be different though. ISO probably should be taken into account as dark current would also be amplified by the higher ISO.
Additionally ISO is not done the same way all the way to the top of the range. There is a point where the amp is maxed yet that is not the highest ISO. At that point there is something done in the ADC (analogue to digital converter) to create an artificial ISO boost. That level is often know by DSLR imagers. For example on the Nikon D800e its ISO1600.
Greg.
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