What would you all think of making a Cover element? An element that has zero functional purpose besides as a second visual layer, for covering/hiding materials beneath it. It could obviously be hidden/removed, but this way you could decorate boxes that make decisions with wires, and only show the wires leading in and out, or hide the lava chambers and whatsits.
This would technically mean you wouldn't be able to put Cover material overtop of walls, but I don't see where that would be largely necessary, though it'd be awesome. And confusing.