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So long as the focuser is not moved by much it should not impact flats unduly. In general you should not need to worry about averaging the position of the focuser over several focus runs, I just use the position from the last focus run of the night.
What other calibration frames are you using? I find with my ASI2600 (Either of them, I have a colour and an OSC one) that lights shot at low gain can be pretty nicely calibrated with a master bias and a master flat (Which itself is normally calibrated with either a master bias or master dark-flat) but if I shoot at high gain, the corners are over corrected unless I calibrate the lights with a master flat and a master dark for the relevant sub length and temperature. I had been being lazy as I have recently found myself shooting a sub length at high gain that I did not shoot darks for.
What I am fairly sure is happening is that the high gain setting, while it reduces the READ noise of the sensor to a lower level than low gain, effectively increases the impact of dark current. The low gain is about 0.8e/ADU and gain 100 is just over 0.2e/ADU so nearly four times the gain.
At a dark current that equates to about 0.2e in a 300 second exposure that comes out at about 1.5ADU, which you would not recon would make a difference in even a stretched image, but the images I did not have darks for (That I mentioned above) had over corrected corners, I shot matching darks overnight last night and applied them to one of the problem integrations this morning, perfect!
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