To Vincoof:
...accompained with a bunch of "Difference Clouds"...
But for small texture sizes (like 64x64 or 128x128) - such picture would look ugly, for there are A LOT of clouds (which are not linked with each other) on one picture... so the advantage of single texture per single cloud is - quality...
the other advantage is that when You have a system of clouds on one texture - their relative positions are bound, and the result is completely unreal visualization... When dealing with many single textures-clouds you may move them more realistically, rotate to make them look differently, resize and so on - so You have more freedom!
Good luck!