an interesting article; pointing towards the "natural" preference of quantity rather than quality.

Perhaps the mutations have to be more specific or directed as the genes are responsible for activity closer to the heart of the system(s). As the purpose becomes more specific or limited.
Or where a large number of variations are applied over a common pool, in groups from a common ancestor.

Give a whole bunch of organisms a phenotype that isn't optimal, and there's a good chance one or more of them will come up with an easier way. Perhaps it could be considered to be a challenge