That's beautiful.
Also, I know the exact trickery you're using because I'm totally going to do the same thing in my map, I think.
Don't you just make it so the skybox is an exact replica of your map, so when you're in the next stage you can't see it, because it's covered by world brushes anyway?
If this isn't it, I have no idea. But I love the custom models and the wires and...oh, everything. The cliffs aren't even boring! There's enough variation so you can't see any tiled textures. Love it. Can't wait for the beta!