1) is there a program or way to read the camera out in 12 bit mode that way I can do photometry / science with the camera
Yes, Sharcap3.0, Firecapture 2.6, can use 12bit ADC, and record under RAW16.
Under SKYX, MDL, you can record it at RAW16.
2) in 8 bit readout mode are the ADU truncated at 256 electrons or is there some type of reduction going
on to allow for the full range but with less resolution (4096 vs 256 readout)
8bit is only for planetary imaging, when you use high gain.
3) in 16 bit readout mode are the ADUs extrapolated to 65536 in some creative way?
Yes, each value X 16.