I've never baked a texture, but I had a similar idea, just take the texture map into Photoshop and add the black spots.  I have done that kind of thing before, no problem.  The advantage of the "Fractal Noise" is that I could change the degree pretty quickly, e.g. as the plague progresses.  And I'm curious in general about the noise functions and how they map to shapes during animation..

But thanks for the suggestion, I'll give it a look.