Yes, one would use Rt for both torque and speed calculations.
Think about it: The speed of the contact surface of the tread is the speed of the contact surface around the wheel, which is the wheel's rotational speed times Rt times two pi.
Also: if your treads are thin, it's not certain that the Rt-vs-r will matter much, because you will get some slippage when driving, and that represents an error term that may be bigger than the Rt-vs-r difference.