This is an interesting question. First of all, what are commonly called simulators are just traffic plug-ins - essentially a set of parameters that are used to control the behavior of the Maxis traffic simulator. Some things can be changed, some things can't. One of the things that can't be changed is that the game is not really completely 3-D in many aspects. For example, if you have a simple train line running diagonally under a viaduct rail which is straight, trains may switch from one to another as if the two rail lines were on the same level. In the situation you mention, although unexpected switching doesn't happen, the game does see the two road tiles as occupying the same space, and calculates congestion accordingly. This is visible in the congestion display. I have seen an example of this with a road crossing an RHW, where the RHW would get congested as it approached the overpass from either side, even though there were no entrances or exits. Assuming this is being treated as a standard intersection, the RHW squares directly under the overpass and the two squares of the overpass itself would have a combined capacity of 20,000 per RHW direction. But one square away from the overpass, the RHW's capacity would be 4000; two squares away, it would be 8000. And although this effect occurs with all traffic simulators, it is somewhat stronger in Simulator Z because Simulator Z has a larger intersection effect. On the other hand, Simulator Z has larger capacities for the RHW-4 than the equivalent capacity versions of Simulators A and B - about 40% higher in the example you mentioned. This tends to ameliorate the intersection effect for the RHW somewhat. There's a table in the first post of the RHW thread on this page showing the capacities of the different versions of the various simulators, so it's easy to compare all of them. Also, the speed limit for RHW roads is 20% higher in Simulator Z than in Simulators A and B, so what Sims lose in congested traffic, they tend to make up on the open road.
Also, I just checked the latest releases of Simulators A and B, and the bug that causes congestion to be severely under-reported is still present in both simulators. This makes their congestion display essentially useless - everything is almost always shown as green. I'll have to mention this in the proper place...