Ahhh, how troublesome. Was thinking of doing some skyboxes myself sometime, but it sounds like they might be rather pesky to deal with.
Skyboxes really aren't that pesky to deal with.
1) You need a big hollow box (though I like spheres better for newer ones)4
2) Flip the normals. (Wait, what?) Turn it inside out. I'm not sure of the normal procedure for this, my method is relatively quick and discovered by accident (mirror the thing and reset x form), I'm sure there's a better way.
3) Save it like a placeable. The thing will automatically end up self-illuminated in-game.
4) Add your model to skyboxes.2da, in all four time columns if it won't change (and set cyclical to 0 instead of 1 in that case)
5) Add your new 2da and model to your top hak. Use in the toolset.
Skyboxes get centered at location 0, 0, 0 of the area (rather than the area's center point), so make them big. I recommend making them very high, if not spherical, just because many people now play with unlocked camera angles. With spheres though, you need to be careful about stretching closer toward the zenith (top point).
Fester Pot:
I saw that when the video was first put out years ago. Not sure if it's a placeable or animated skybox (I haven't tested yet if you can animation part or all of a skybox). A working file was never released to the public.
Either way, the clouds are all circling around the PC or area. Looks fine from one side, but turn around and the other nearby clouds are moving in the opposite direction? Weirds me out.
Now, if someone were to get it to work inside a GIANT torus with non-repeating clouds (so all clouds on all sides appear at a long distance and move in the same direction), and slowed down the cloud movement a lot, then it would be much more believable.