See the section called Model Simulation Callback Parameters.
The StopFcn callback will execute when a simulation stops by either running to completion or is stopped by the user.
When you use exit, that is simply going to close MATLAB entirely and the execution of the StopFcn callback is a moot point.
Try a simple test:
In a models StopFcn callback define a variable such as x = 10. Then run the simulation using sim or just pressing the simulate button. When the simulation runs to completion, the variable x should be defined in the workspace.
