i can't really answer #1, i think michael covington forked BPP (to create BPPFD) to add flat darks for DSLR processing. he's around her so i think he can answer.
if you want to use BPP with dark flats (or flats where the ISO/Gain is different than the lights) what you do is load some dummy lights, but load your real flat darks and flats and run it. this will result in a calibrated master flat file which you can save somewhere and then run BPP again with your lights, darks that match the lights, and the master flat. you just need to tell the script you are using a master flat (there is a check box).
usually CMOS cameras have some amp glows which preclude scaling of the darks, so there's no reason to use bias frames. i think your best bet is to always acquire matching darks for the flat and light durations and just skip bias frames. having said that i don't use a CMOS camera so maybe ASI1600 is an exception and scaling the darks would be OK.
rob
