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IMHO, flat is a file with informations about the differents responses from pixels of sensor. Same intensity of light cause differents output level from each pixel.
If your flat was done in the right way, e. g. with equal distribution of white light over sensor, it is normal that you observe diferents levels in the flat image.
The optic, vignettting, and dusts cause artificial pixels (sensor area) level output and will be showed in the flat image also.
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