I think that Black's point of the cytochrome C case was that there are multiple variations of the protein which are completely functional. Therefore trying to perform probability calculations on the formation of a specific version of cytochrome C is pointless. It ignores the fact that a large number of possible outcomes will give a functional protein. Therefore the probability is not say 1 in 10 million but 500,000 in 10 million. Spetner apparently ignores this point because it defuses his argument.
As you rightly point out, the variation found in cytochrome C throughout living organisms is consistent with the theory of evolution: a primative protein which has only a small, critical functional zone and where mutation can occur outside the functional zone without being selected against.
Makes on wonder why Spetner's intelligent designer couldn't stick to a single "intelligent design" for the protein.