Would impact the FPS a bit, but it’s doable. I looked over your thread on the ET forum also.
First, if you’re using indexmaps and so-forth, read up on AlphaMod brushwork here in the q3map2 forum for a much more straight-forward way of controlling the blending on the terrain.
Second, I’ll assume you’re using $lightmap-last terrain.
Third, yes, it’s possible to do what you’re asking about. I’d personally recommend using a ‘blendFunc detail’ pass after your $lightmap pass on your terrain shaders, with a copy of your cloud layer adjusted to 96->192, with the midpoint set to 128 in the Levels tool in Photoshop. This will allow it to act as 75%-150% brightness on the terrain, which should be conservative enough values your ‘static’ lighting will remain dominant, and the cloud layer effect won’t “blow out” your colours anywhere. If the above doesn’t make any sense, feel free to post the cloud layer you’re using, I’ll build a ‘blendFunc detail’ that I think will work. Unless your cloud layer is being applied with ‘blendFunc add’ currently, merge your cloud layers to a background of (128,128,128) first, also, as (128,128,128) is ‘fully transparent’ with ‘blendFunc detail’ on 99% of video cards.
Then you just need a tcGen/tcMod pass applying the cloud layer to all of your terrain shaders, as a final pass after the $lightmap pass. Matching it to the overhead cloud layer would be purely a matter of guess-and-try unfortunately though, the values for the “tcGen vector” and “tcMod scroll” will have to be found by experimentation.