I can send you a model, but it doesnt explain the situation (my model is typical tower structure of L sections). I just tried an example with L120x10 (class 4) like a very short column (0,2m) which do not have any danger to loose its buckling resistance, but i put an axial force to obtain a maximum streeses or near it. It also calculate like a section of class 3 instead of class 4...
If we look at p. 5.5.2 (9) of EVS-EN-1993-1-1 (your quatation) then its wrote that we can take class 3 in consideration EXCEPT as given in 5.5.2 (10), and p 5.5.2 (10) is about buckling resistance of elements, where sections of class 4 exist and its area = Aeff.
Finally, can you bring me an example when robot calculate section of class 4 as a section of class 4 with real area Aeff?