PID Tuner app (pidtool) was never intended to be used like you describe.
If you want to process multiple plant models in a batch mode, use the function pidtune, which is the command-line equivalent of PID Tuner app. The function lets you specify plant model, and the values of tuning knobs (bandwidth and phase margin). You can call this function in a for-loop or you can call it on an array of plant models so it returns an array of PID controllers.
Take a look at this video , the first three minites show how to get a set of linear plant models from a nonlinear Simulink models, but after that the video shows how to design PID controllers with pidtune in a batch mode.
