First off, wanted to say, I'm a big fan of this visual pack and appreciate all the hard work you've done for it. I was looking at the different configs and noticed that clouds atmosphere heights differed, and this may be what some people were looking for. Here it is with the standard config:
And here it is when I edited the main cloud's altitude to 7000 and the cirrus layer to 6000:
Now I may be missing something, but I thought this might help.
Another example: