With Strand, the integration is over the area that is displayed. So for a stiffened slab, it would be necessary to display the width that the code allows.
I often model steel plates with stiffeners for materials handling chutes and bins etc. I always put the centroid of the platework on the centroid of the beam elements. I do not bother to take the increased bending strength from the plate into account at all. This is an appropriate conservative approximation for this application.
I will explain my use of plate elements for both the slab and thickened slab in a little more detail, as think you may have misunderstood me. I would only use one layer of plates for both the slab and one layer for the thickened slab. This means that I do not need to integrate to calculate moments. I simply offset the plate elements so that the top-of-concrete is the same for all elements. The offsets are a built in variable in both beam and plate elements, so that the nodes can all be in any single plane, whether the centroidal plane of the slab or the top-of-concrete. I suggest a little caution for the results at the change from 1 depth to another, but I would have confidance in the results away from the step change. I have not attemted to benchmark this method, but it seems to work well, the results look good.