About flickering of textures. I suspect the increased opacity enhances the visibility of the inherent flicker. I'll look more closely at texture size (via reduction of the .tga to 512 pixels), to see if this is a factor as well. Has anyone tried the hi rez clouds, which use a 2048 pixel .tga? I note that its textures are quite translucent indeed, which perhaps helps on the flicker front. What if one boosted the brightness of their alpha channel, until the brightest parts are just reaching full white? I can't play with the hi rez stuff, myself, else I would delve into it...
If increased cloud opacity is the flicker-enhancer, I can begin to see a reason for the two-layer approach, and the building up of clouds from numerous textures. Many translucent textures overlapping have increased opacity where superimposed, thus making up for the singleton's gauziness. And the second layer builds a superimposed cloud with all textures now doubled up.
For higher-end machines, one might profitably exploit the second layer, by having its draw distance increased. These textures can be quite small; certainly 64 pixels individually, probably 32, and possibly 16 ( for 4x4 matrices of 256, 128 and 64 pixels, respectively.)
By such an approach, one may employ more semi-transparent textures if indeed this is the antidote to prominent flicker.