Found a way to do this without needing to duplicate textures. However, this will not currently work with nwMax Plus. It will work with VelTools.
For any alpha texture that you want to render properly, you will need to make the following changes in the Material Editor:
For the Diffuse Map, expand the Bitmap Parameters rollout and change the Alpha Source setting from Image Alpha to None (Opaque).
Now apply the same texture as an Opacity Map, expand the Bitmap Parameters rollout and change the Mono Channel Output setting from RGB Intensity to Alpha, verify that the Alpha Source setting is Image Alpha.
You should see the effects of these changes in the Material Editor's sample slots and if you have a perspective viewport, you should see the changes there as well.
When using VelTools you should hide any non-rendering meshes, and ignore_NGon triangles prior to creating your minimap, VelTools will hide helper objects, (not sure about emitters).
Not fully tested, so I would suggest exporting your tile, and saving your work prior to making the above changes to any materials.
If feedback is positive on doing it this way, I can look into having nwMax Plus programmatically apply these changes when loading the tile during the Minimap Maker process.
VelTools works with tiles that are in the current scene. In theory, you could load an entire tileset and VelTools would create a minimap for every tile that was parented to an AuroraBase helper. I say "in theory" because I have only tested it with four tiles.
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MDA