Hi Steve,
I also used a EOS 600D (T3i) for astrophotography. My camera is modified (filter exchanged). I don't use BYEOS. If I understand it correctly, BYEOS saves all images in Canon's raw file format, CR2.
Obviously BYEOS does not display a linear histogram, so it is not suitable for judging whether the flat frames are properly exposed. However, the PixInsight histograms that you showed are not from the raw data as well: they are histograms of debayered flat frames. If you want to judge the intensities of the raw data you have to take a look at the raw monochrome Color Filter (CFA) images.
I would do the following in order to properly check the exposure of the flat frames:
1) Set RAW format preferences to 'Pure Raw' (Format Explorer, double click on 'RAW').
2) Load a flat frame. You'll see the monochrome CFA image.
3) Call HistogramTransformation. Set plot resolution to 16-bit (64K) and horizontal zoom to 4 (with this setting and the slider left at the leftmost position, you are viewing the rabge of intensitiaes from 0 to 16383).
4) Call ImageStatistics. Set 16-bit (64K) and uncheck 'Unclipped'.
The range of the intensities is 0 - 16383 as the camera has a 14-bit AD converter. The T3i has a bias offset of 2048 ADUs. With my camera, saturation occurred at about 15300 ADUs. So the usable range of intensities with this camera was 2048 to 15300 ADU. The center of this range is at about 8700 ADUs.
The linear range of modern DSLR cameras is quite large. You want the exposure to be plenty, but must avoid safely that pixels will be saturated (disregarding the small number of hot pixels).
I suggest you not to attenuate the R and G channels by red cellophan. Who tells you that this material is sufficiently homogeneous and does not introduce artifacts to your MasterFlat? Set the exposure so that the mean of the flat frames is around 8700 ADUs with the settings given above (see appended screen section. This is simple and worked well for me. It is not fatal that the red channel is somewhat weaker than green and blue ones.
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Why were your flat frames debayered? Definitely all the calibration (and optionally CosmeticCorrection) shall be done with the raw data, i.e. with monochrome Color Filter Array (CFA) images. Debayering shall be performed just before the alignment step.
Bernd