Posted by: @chrisl

1) When directly using the NEF-files to create a master flat, the MF turns out to be a greyscale image with an odd looking pixel pattern. Is that correct?

 

Yes. If you zoom in on a RAW (NEF for Nikon) image without RAW processing, you will see a the colour filter array (CFA) pattern. The RAW image is actually a greyscale image. Its the position of the pixels that determine whether the pixel is a red, green or blue pixel.

The master flat is an averaging of the RAWs, pixel-for-pixel.

Posted by: @chrisl

2) When converting the NEF files into TIFF and creating a master flat, the MF is a RGB image and displays as one would expect (vigneting, dust artefacts, etc.).

3) Why is the MF so different (greyscale vs. RGB) when using NEF or TIFF?

 

You are not supposed to convert the RAW because then 4 grey pixels representing R, G, G and B are blended into 4 colour pixels, each one containing R, G and B components. To calibrate your lights, you use the RAWs to create a master calibration frame that is applied to the light RAW, pixel-for-pixel grey level before colour conversion.

Posted by: @chrisl

4) When using NEF, does APP account for the orientation/rotation of the frames? Does APP rotate the individual frames when they are originally orientated differently, before creating a master flat?

 

Regardless of the orientation of the picture when taken - this is meta data in the RAW file, the RAW file image data will always be the same, so orientation is always relative to the physical sensor and so does not need to be considered in calibrating and stacking.