vicent, if you are still reading this -
i have read that a 2nd reason for using flats is to correct for differences in QE from pixel to pixel. now, i have no idea if this is relevant on a DSLR given how much 'cooking' is done on even the "raw" files.
so yes, the vignetting will be the same at ISO100, but how about this QE normalization? any idea if this really applies to a DSLR? if so, it seems that you'd want to use the same ISO for your flats and lights.
in any case it seems the effect would probably be pretty minor, even for an astronomical CCD...?