That Support Center article is a few years old and might need to be updated. The crux of the matter is that if you have specified a layer as a plane layer in the stackup editor then the trace modeler always considers that layer as a solid continuous plane. This is often a good assumption, but not if you have a layer that has, for example, a large area fill over half the layer and routing on the other half of the layer. In this case, you want the section of the layer with routing to NOT be considered as a plane for the trace modeler.
In HyperLynx SI, I think starting in VX.2.3, we can specify parameters for area-fill coupling. This method is a more general solution and correctly handles the situation I described above. So in current versions of HyperLynx SI you can leave layers of mixed planes and routing as a signal layer, configure the desired parameters for coupling to area-fills, and the trace modeler will create the correct model in the various different geometries.