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That is what I was getting at to an extent. If all you want to do is remove issues caused by the optics then the ISO doesn't matter. This includes dust bunnies, vignetting and optical light fall off.
For technical images where you're wanting to do astrometric studies you do want to keep the ISO the same so as to not potentially introduce any inconsistencies. Flats are not just a map of what has already been mentioned but physical pixel of pixel sensitivities irrespective of light fall of. This is a part of the sensor and therefore changes in ISO have the potential to change stellar magnitudes. Not by much but potentially enough to reduce accuracy when trying to get millimagnitude accuracy.
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