Thanks for the additional explanation, which was quite helpful. I just noted that Raw Therapee also has a flat field operation which works directly on raw files so the gamma compensation problem is avoided. It has a filtration option and one can use a low value to remove dust spots.
Indeed, just as the doctor ordered. A low amount of blur to preserve some (dust) detail, yet reduce noise influence, and a larger blur to eliminate higher spatial frequency signal. Of course there are better ways to remove detail than a simple (Gaussian) blur (which e.g. literally meets it's limits at the image boundaries, something that e.g. ImageMagick can deal with by activating 'virtual' pixels).
If one has a low noise image, larger blur amounts are not needed. One can apply the tone curve and other adjustments directly in the program.
One thing I don't know with this facility and with the LR flat field plugin is what exposure is needed for the flat field image.
Exactly, that's why I would recommend to shoot one's LCCs or FF images at a lower (native) ISO ETTR level, exposed just short of clipping the tail of the shot noise. The lower the relative noise level is (and thus the higher the S/N ratio) the easier/better the postprocessing and number crunching can be.
As you mentioned the brightest areas should be white, but this could be adjusted by an exposure compensation for the flat field raw image so that one would not have to bracket or otherwise fiddle with exposure.
Correct, the sofware should normalize the input data, but it 'won't hurt' to maximize the image's S/N ratio either. At lower ISOs, it should help to +EV correct a camera metering of a uniform surface by 2-3 stops before the shotnoise tail clipping becomes an issue.
I don't know if this is done in either program, but a bit of experimentation could determine this. I don't know if a two pass correction is possible in Raw Therapee.
Since RT is not layer oriented, I doubt it, but since I use Capture One for most of my Raw conversions, I haven't tried the RawTherapee Flat Field corrections with moderate blur radius settings. It may be possible to find a good compromise.