I know with ThunderRIO we can still develop for the cRIO.
My question is this: Is it possible to communicate using WPILib or something like WPILib to PWM motor controllers, solenoids, CANJaguars, etc., without having to use the IterativeRobot/SimpleRobot/FRC Communication Protocol? I.E.; a robot fully autonomous and not connected to a PC, or a robot using a roll-your-own communication protocol?
I believe the virtual RobotMain() function in WPILib can actually help you with that. I’m not entirely sure though.
The issue with doing this is that the FPGA is what actually controls the motors, and the way it is programmed from FIRST requires a connection to a driver station to do this. So the only way to do it without having a connected computer would be to rewrite the FPGA code. Another option is to put a computer running the driver station physically on the robot, but make sure if you do this you still have a way to kill everything if something goes wrong.
There’s nothing stopping you from writing a driver station client on the robot and connecting it to localhost 
There’s a few open-source driverstations out there, just pick your favorite & run it on the RIO. Disabling is the only part that worries me.