As far as I know the PWM signals only tell the Jaguar to adjust it's output voltage, there is no feedback from the motors to the Jaguars. I do believe that you can wire say a limit switch directly to the Jaguar to make it stop or start (or brake or coast) but I know of no way to hook an optical encoder-type device to the Jaguar directly.
We are using Holonomic Mecanum drive this year and it functions fine without using a PID loop to adjust the wheel speeds (although we did that last year for traction-control
).
Good Luck!