most newer DSLRs have 14-bit A/D converters. PI brings these 14-bit values into a 16-bit space, so a completely overexposed flat loaded in PI will have it's histogram crammed up against the value 0.25. so 1/2 well depth would be 0.125 in PI's histogram. other programs may be different (they may scale the data) so it's best to find out where the histogram lies when you feed the program a completely overexposed image.
if your camera has a greyscale setting, never use it. that will result in the camera debayering the image and converting it to greyscale before it's handed to you. that makes the file useless as a flat. just shoot your flats as you normally would.
some confusion stems from the fact that *all* CCD images are mono images. when using a mono camera, you make 3 images (R, G, B). with an OSC (one-shot color) like a DSLR, the filters are basically glued right on top of the sensor. there 3 filters per square block of 4 pixels, and there are 2 green pixels per block. if you open one of these images as "raw cfa" you are looking at the data exactly as recorded by the sensor. debayering goes in and "deinterleaves" the pixels into 3 planes and assigns the color R to one plane, G to the other and B to the last.
rob