Hi,
I will be posting a question with regards to a topic not far from your question but meanwhile this is the way that I do the image integration to avoid getting the noise from B and G channels in the R ( Ha ) Channel. I use BPP script.
Set the BPP to calibrate only and add all the usual files. Set the debayer to SuperPixel and carry on as per normal. Then once BPP has finished its stuff close BPP and go the directory that you specified in BPP. Now using Batch Channel extraction on the Debayerd files, I think they have a suffix of d, extract the Red channel only and dispose of the other two. The files will have a suffix of red at the end their names. Now open Staralign and register the RED files and then use image integration to combine them. You should end up with a master Mono Ha file and you should have nothing to do with CFA configuration rather than setting it to SuperPixel for debayering. My prolem is whether the flats need to treated differently for this process as the B and G channels affect the exposure length of the flat and cause over correction.
Regards,
A.G