Hi Dune,
I'm not sure if it has been fixed, but it's better to raytrace the atmosphere (defer atmo/cloud on) to avoid pole problem (missing pixels like pokoy describe).
I do prefer stereographic projection, aka fisheye in terragen, even if you want to reproject it as cube map or spherical.
The big advantage with stereographic is that you have full resolution on the pole.
https://www.behance.net/gallery/32096159/Terragen-stereographic-skiesIn fact you even have more resolution on the pole than the horizon.
It's also the kind of image that is easier to manipulate (paint-over) in photoshop, because there is not really stretching area, and there is no seems (compared to spherical)
It's the perfect projection for first person shooter, maybe a little bit less suitable for racing game where all the attention is on the horizon line.
Stererographic skies need to be reprojected on an half sphere, UV's are just made using planar Y projection, then relaxed.
I can provide you a simple model poly sky model with the right uv's if you want.