I think it is a variation on the problem that has plagued all versions of the sim that I have known, that of transparency and display order (I've faced it recently with my aircraft canopy, and previously with propellers).
I can't guarantee what I'm about to say will be of any use (I've limited experience and I make simple things, so I only push a boundary when it is absolutely necessary), but one of the things that helped me with the canopy was cloning the transparency, putting the two cloned surfaces fairly close together and flipping the normals of the clone that was behind the canopy so that they faced inwards. In itself, that is meaningless for you, but would a variation on that idea enable you to mask out backgrounds? For example if you make a planar object that you've put light onto, what would be the effect of having another plane behind it that is more opaque but has nothing on it, perhaps made transparent using alpha - the sim would see it as a solid object because it can't know that there's an alpha channel making it invisible. There's be no clouds rendered behind it because of that. The trouble then is that there would be masking of scenery objects, but that is something you have more control over.
When I had intractable problems with systems in my IT career, I sometimes had to adopt the approach of trying to force the problem into a kill-zone where I could actually make a difference - sometimes by redefining the parameters of the problem in incremental steps to morph it into one I could solve, and that's all this is.
Your new problem of scenery masking could possibly be fixed with small opacity adjustments of the alpha-ed object, or maybe even a simple thing like alphabetised texture names that enforced a particular draw order in-sim.
Its just a thought. Don't waste any time on it if you think it would not work, or is a rubbish idea.