The noise estimates for the red, green and blue channel are stored inI am curious about this. First, what are the xx in NOISExx?
NOISE00, NOISE01 and NOISE02
From the ImageCalibration documentation:This is a color image and I would have expected if there would be multiple noise estimates.
Does DeBayer change the noise characteristics, and if so would it be better to use noise estimates generated by that process when applicable?
The resulting CFA mode is also used to calculate the noise
"ImageCalibration will compute per-channel noise estimates for each target image ... Noise estimates will be stored as NOISExxx FITS header keywords in the output files."
So I was expecting it to produce NOISE00, NOISE01 and NOISE02. Did you have 'Enable CFA' selected? If it wasn't, it would think it was a mono image, and only create NOISE00. I think the bayer pattern would then have a strong influence on the estimated noise. Please let me know if this does not fix the problem so that, if necessary, I can adjust the script.
Ideally we would prefer to have noise estimates from before the debayer process, but I see that there is an 'Evaluate noise' in the Debayer tool, which will produce the NOISE00, NOISE01 and NOISE02 FITS header entries.
During registration, if the image shift is half a pixel, the registered pixel interpolation will use a equal contribution from the neighboring pixels. This has a maximum noise smoothing effect. If the shift is zero (the registration reference frame), there is no noise smoothing. I assume that a pixel shift of 1/4 will have about half the smoothing effect of the 1/2 pixel shift. If you dither you images, the smoothing effect will depend on the dither shift.Finally, in your chart it seems curious that the two series do not even move in the same direction from frame to frame. For example, the red line decreases from  to  but the blue line increases. This seems surprising if the cause of the difference is simply registration.