Nebulas don't work that way. Nebulas are drawn additively, i.e. the color you see is the sum of all the nebulas being drawn in that spot.
The game engine detects if the effect has an alpha channel. If it does, it draws it like a planet. If it doesn't, it draws it as a nebula. If, however, it's an indexed-color .pcx image, it will draw it opaquely but with (0, 255, 0) green as transparent.
But that's a different kind of nebulas.
Speaking of the .neb kind, I finally got Nebedit to build, but it doesn't seem to do anything and I can't exit it once it builds. I think it might be because I'm debugging, so I'll try turning that off, but if that's the case, there's no way to debug it...