Also the tune can modify your pedal as well. Not sure if that's one of the adjustable options available in the tuner. I'd have to go out and check. I found I didn't want to amp up the pedal after I got the tune. It didn't need it to feel responsive.A real tune isn't going to have occasional power loss from the ECU limiting torque, in any weather. The JB4 can only intercept & modify the signals that it taps into, whereas a tune is literally clanging the operating logic on the ECU. It is a more direct and accurate way of making modifications, and it's exactly how the manufacturer controls your motor (well, with the ECU being locked).
The Pedal Commander can't change how the ECU interprets the pedal signal, it can only "enhance" the existing signal by making it go to 100% earlier (basically the pedal commander can't do anything your foot couldn't do already).