I second not to use skyboxes anymore. Skydomes are the way to go. You can use hdris at it out of the box so to speak. Terragen is cool. But every 3d package with volumetrics should do the trick too. Blender for example. It's not even more work, dependant of what you want to achieve.…
Do the skybox clouds need to be animated in-game? Or is it mostly static? If animated, you'll likely need a very performant solution that relies on a layered shader and a combination of static and scrolling textures. You don't want it hogging resources. There's no out-of-the-box solution for this afaik. As an example, this…
Terragen imo for procedural clouds. But it takes alot of tweaking, deep node system diving , lots of forever rendering and post compositing . Usually it's good in one sector of a sky and absolute crap in other. So compositing is a key thing anyway. It has spherical camera to render . A box is a worst shape for a sky really…