Karl,
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I do not use Flats as it used to generate more problems the it solved.
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I have found the use of flats is very important, as the illumination varies across the frame. Perhaps it is not such a problem with a small region of a small sensor, but I expect still a problem, as there can be dust, etc.
It is important to take the flat of the exact optical configuration that was used for the science images, so that means no changing filters, removing the camera, or anything, until the flats have been taken. I use a "T-shirt" diffuser and a LCD panel computer monitor for flats, and it has been working well for me.
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For photometry I use only about 1/3 of central image area. I believe that PinPoint automatically compensates for atmospheric extinction, but I better check it up.
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Atmospheric extinction is a significant factor, it must be taken account of for absolute photometry, so yes, do check.
Ivan