Well, ,changing the layer's altitude is all I can think of, really. BUt the results can be unpredictable, because while changing the altitude of the layer, you are also modifying the density function, since this function is evaluated in world coordinate space. Whcich means that each point of the function is evaluated according to its location in world standard space coordinates. This point will then given a density value. When this point is moved in space by changing the layer altitude, the density evaluated for this point now depends on its new location, and can be different from what you had before. This is a problem for what you want to achieve, but it's the magic behind animated clouds.
Another workaround wpuld be to modify the aerial perspective over time, so the cloud layer would fade when AP values get higher. Not sure this would animate (never tried), and not sure it would look realistic either, because it would add a lot of haze to the scene over time.