It is a common question, and source of confusion. Maybe the following FAQ document can help you clarify the input/output selection:
The program is modeling the system process, not the controller. Try not to get confused by the names of the variables for any specific implementation, what the PIDTuner considers “input” is the input to the process (output of the PID). And what the PIDTuner considers “output” is the output of the process (input to the PID).
Hope the information above makes things a little clearer.