A beam model is a high level abstraction that captures bending and shear behavior of structures of uniform cross-section. As long as the correct moment of inertia is used, the beam model will be fairly accurate for the deflections of the beam. Note that the beam property must use the moment of inertia about the nodal location, not the moment of inertia about the centroid. In your example, the centroid jumps up when the beam cross-section changes from rectangular to stiffened cross-section.