I've got the SOLUTION !!!!!!!
You have to choose the model to apply in you simulink based on a workspace variable "model_choice". And this variable is the parameter to varry in the Control System Tuner App.
Detailed Explanations:
-Add the "model_choice" variable to your workspace :
model_choice = 0
-In your loop you want to tune, just add a parameter called "model_choice", and replace the identified model with a subsystem as following:
-In the subsystem, add an "Index vector block", in order to be able to choose which model to use, depending on the model_choice variable.
Here, if model_choice=0, the motormodel1 will be applied. If model_choice=1, it's the motormodel2. You can add as many models as you want.
-When you have this structure in your Simulink, simply use the Control System Tuner app, and in parameters variation, choose the parameter "model_choice" :
Tadaaaaaam, tune both models as desired:
As simple as that !