I have created a model with a 8 layers and four scenes. In one scene, 5 layers are visible, while each of the other three scenes have two layers visible. When I change scenes, the layer visibility indicators (the little eyes on the left of the scene names) do not change to match the layers that are actually visible. This does happen and works well in Make versions.
This is slightly confusing so, hopefully, it will be rectified by the programming team, but for any other teachers out there, be aware that it is happening and warn your students accordingly.