done is a configuration pin and it gets driven low by the FPGA when the FPGA has not completed/startd configuration. Once the FPGA configures it's driven high by the FPGA. It's not an I/O pin.
For B the R193 isn't for power it's a pullup. The TI part probably has an open drain output (didn't take the time to check) so you can wire or them together for a single power good signal for when all the supplies come up. When all the TI controllers say power is good the open-drain stops driving and the pullup resistor enables the FET.
For C not sure why that was done. I think it should be a pullup to the VCCINT supply not a resistor to ground, that just burns power. Maybe they wanted a hand warmer ;-)
Wait a minute, I suspect it's to detect power on the VCCINT supply. If VCCINT hasn't come up the LED won't light, since the gate is pulled to ground, VCCINT has to be up before the LED lights up.
Regards