"That may still be truly random, only that the underlying distribution isn't uniform. Having a uniform distribution isn't all that important as the distribution may be changed by looking at things differently.
And if it happens in the same areas across related species?
Capacity for mutation need not be random. Individual mutations may be. The "randomly chosen" mutation in each specific instance still follows the distribution of susceptability.
A uniform sample of two unequal regions will still have more points from the bigger region.
My point is that the term "random" does not imply a specific distribution.