"Only transparent texture I know of is the lifelogo, monlogo, npclogo. It's a dark purple color that does not show up in game.
The texture in question is called "nothingatall". It is RGB color 128 0 128. If you open a unit in 3do builder with all the TAK textures, you would see that the transparent texture is the nothingatall texture. Ex: Lodestones have a transparent background. Basically, they just pasted a picture onto that background and used that as the unit. So you would have to figure out how to add it your palette and once added, use that color to color over parts you do not want showing up in game.
Also, the set white to transparent in GB Pro or GB is for TA. Apparently, TA's transparent color is a bluish color. Just open a TA Gaf explosion file and extract all the files using the TA palette and you will see blue as the background or transparent color."
If you can get MSPaint to create that color, it should work. If not, use another photo editor, such as gimp or xn view, etc.
Vaerun