This process is to use the flat field illumination source as both the image and the flat field. If you take an image of a completely uniform (idealized) light source, then the image you get would be a faithful representation of the vignetting of the imaging system, the dust attenuation, and the pixel-to-pixel variation of the camera's sensor. If the uniform light source is not completely uniform, then you will introduce errors in your calibration, because the whole process relies on the uniformity to work.
That being said, no flat field light source is completely uniform, and characterizing the spatial non-uniformity is an important step to understanding how good your final image can be. To answer your first question, we need to understand the source of dust on the imaging train, and how it might affect the final recorded image. There are essentially three places where dust will impact the image:
1. on the sensor,
2. on the sensor cover glass, or
3. on the filters placed in the light path.
1 almost never happens because the sensor is sealed and evacuated in most cameras. So we are dealing with 2 and 3. Dust on the objective or on the corrector is so diffused over the entire focal plane that it has no noticeable effect.
When you rotate the camera and filter wheel, the relationship between the dust donuts and the sensor does not change, so the only thing that changes is the view of the light source. In other words, as you rotate the camera/filters, any spatial non-uniformity of the light source should rotate on the sensor. Important note: if the non-uniformity is radial in nature, then this technique will not spot it.
Now if you use the light source as the flat field image, and then rotate the camera and take another image of the light source, you should be able to see non-uniformity because if your light source is not uniform, your final image will be under or overcorrected so when you go look at the line profile of pixel values across the image, there will be some differences along the line. Remember, if your light source is perfectly uniform, there should be no impact from rotation, since at all angles, a perfectly uniform light source will yield an identical image. The vignetting of the telescope will have an effect if your image sensor plane is not exactly on the optical axis and exactly perpendicular to it, but assuming that you have a properly collimated image train, this should not be affected by rotation of the camera/filter assembly.
As far as subtracting darks vs. biases, you are correct that for short flat field frames, a bias might suffice. You should experiment with your particular camera. Particularly for narrowband filters, exposure times might be in the 30 second range, and it is possible that the noise will accumulate enough to need a dark of the same exposure. I might suggest looking at noise levels in your bias frames and see how they compare to darks of various short durations. If there is no difference between the pixel statistics of a bias and a short dark, then by all means use bias frames.
Generally the accepted equation for calibration is:
final image = [(raw image - dark)/(flat image-dark)]
of course the flat image is normalized so that essentially you are dividing by a number very close to 1. Substitute bias for dark if you have very short images.
The standard deviation of the pixel values of the image can be found from the image statistics. In the perfect world, a perfectly uniform light source should yield an image that has a very narrow range of pixel values. Of course there is uncertainty of measurement, so you cannot ever get an image with identical pixel values, but the smaller the standard deviation, the closer to uniform the original light source is.
Again, remember that all of this is predicated on the following:
1. Image train is perfectly collimated, colinear and the image sensor is perpendicular to the optical axis
2. there are no symmetrical radial spatial non linearities in the image of the light source.
3. the image has been properly dark subtracted
2 is surprisingly common in telescopes due to unsuppressed internal reflections in telescopes these days. If you have a surface that is reflecting that is circular (say a tube baffle), then you will get a circular non-uniformity in the image that will not be sensitive to camera angle. These internal symmetrical reflections cannot be flatted out, but must be removed from the image train itself. You can easily diagnose them by removing the camera and looking inside your telescope in the daytime. for a catadioptric telescope, there should be only the bright reflection of the secondary, with no other light rings, just inky blackness with the secondary hovering in the middle. For refractors, you should only see the bright light from the objective, again just floating in the inky blackness without any bright rings from internal reflections. You will be surprised to learn that the majority of high-end telescopes and accessories have poor off-axis baffling, and are often a problem that can vex the observer who is looking to stretch images to the greatest extent. I myself have seen this from an off axis guider. Artificial flats will exacerbate these internal reflections since there is a good deal of off-axis light from a light source close to the objective.