RR-Track sets up with a 2-inch "bench top" as the terrain base. You can work around that somewhat by going negative on the "Z" axis of the object properties -- filled rectangle with a 48" height as a leg set to -48" "Z" position.) The only catch is that the legs extend below the layout base.
The other way is to fabricate bench top elements as filled rectangles and polygons with a thickness of your choice and set their height. The height you set will represent the "base" position of that item, so a 4-inch thick bench top set to 36 inches "Z" axis would put the base at 36" and the top at 40". You could then use the extruded rectangles with a height of 36" to match the benchwork. All track would have to be elevated to 40" and above and you would have the issue of excessively large "berms" in the 3D rendering (can turn that off or turn everything to "overpass")
All that said, anything I do is with the basic terrain base with the presumption that I'll be adding legs of some given height.