The 3D surface maps do support layer transparency.

To do this:

1. Select one of the surface layers.
2. In the Properties window, in the Material Color section, click the (...) button to the right of Upper.
3. Change the Opacity value for the color(s) of the surface.
4. Click OK and the opacity is applied to the layer.

To set the opacity of the color nodes in a script, use the ColorRGBA property of the ColorNodes object:

Dim ColorNodes As Object
Set ColorNodes = ColorMap.ColorNodes
ColorNodes.Item(1).ColorRGBA.Color = srfColorGreen
ColorNodes.Item(1).ColorRGBA.Opacity = 33
ColorMap.ColorNodes = ColorNodes

Updated November 13, 2018