Within SystemTest the order of execution corresponds to the order of elements within each of Pre/Main/Post test. So a LimitCheck or MatLab code that is run before the Simulink Model (i.e. listed above the Simulink Model, within Main Test) will not have access to the variables corresponding to the output of the model. This gives the variable is empty error.
To sort, click on the LimitCheck/MatLab script test elements and drag them down within SystemTest to below the Simulink test element.