Well, what I did was to select a region with the select tool, and then deleted it, leaving nothing. I didn't intentially set 0's on all the color properties. That's just what happened. And that method has worked in a lot of other scenarios where I needed a transparent region.
I had a thought this morning as to why I got black - I had a specular map in place on that image which is fully black. I thought maybe that was the reason for the end result of black in the cut away region. And it was - kind of. Leaving out the specular map, I got a grey box instead.
And on reflection, I think the issue is that Oolite applies a default specular color to models rendered in game that aren't given a specific specular map, with a default value of (0.2, 0.2, 0.2, 1.0). I guessing, but I think that is why I got a grey box when I left off the specular map.
So, the issue is because we are using a model with a texture applied. We aren't dealing with a standalone image (like a background image or overlay), which Oolite handles differently to what it does in 3D space. Transparency in backgrounds and overlays work just fine. The end result is, if you want cut-away sections, and to layer them on top of each other to build up a screen, we can't use transparency to achieve it. The model needs to explicitly define the cut away regions.