Yes, they really are fractal clouds.
Here's the original section of fractal pattern as generated by the KPT Fractal Explorer plug-in for Photoshop.
The original fractal
And here's the image lightened and color shifted, with the upper area selected and filled with blue. Et voila, clouds!
The resultant clouds
It seems that Chaos Theory and Fractals may be our best tool for understanding complex patterns like clouds and weather, and perhaps even Badnasty Jumpjump. The number on Argon's boat is an equation for the Mandlebrot set.