What you're doing with the command "set_param('test', 'SimulationCommand', 'start')" is the equivalent of hitting the "Play" button the model. The model simply logs "tout" to the MATLAB workspace as an array (not as a scalar). Also, there is no guarantee that tout is updated immediately during simulation - it is only guaranteed that at the end of simulation "tout" is a vector containing the list of all time-steps that the model ran at. Even if "tout" were a scalar and were updated instantly, the line "if tout>3" would have to run at the exact instant that tout became >=3. You probably need to put in some kind of while loop to be more realistic, but like I said, even a while loop will not help in this case.
What you might need to do instead is write something like a MATLAB Function that reads the simulation time value (perhaps from the Clock block) and performs the set_param. You can call this function from one of three MATLAB Function blocks so it is run at every simulation time-step. Alternatively, you could use a solution similar to this FEX submission.
