1 & 2 it should both work. Software generator is for simulation purposes only.
For DC mode you have to adjust Offset setting, not Voltage.
Custom mode analog generator should work. Did you use the custom file: "/data/signal/custom.signal"?
Generator offset should be calibrated. You can change calibration settings manually in "data/startup/calibrate.json".
Yes, there is a bug in FPGA firmware for VCC_DIG output. Firmware is not setting both of the digital variable resistors. This will be fixed in new version. You can also change "generatorStep" manually in "data/startup/calibrate.json"