A simple way to state the problem with Cornelius Hunter’s argument is that he is arguing that a Designer could do anything, so a Designer cannot be refuted by any observation. He is happy to have thereby refuted all the people who point out bad design.
But he doesn’t get it that what he has just done is to admit that the hypothesis of a Designer is not science, as it predicts every possible result. If you predict every possible outcome, the ones that are seen and the ones that are not, then you have not predicted anything!
Unless you have some information about the Designer’s intentions, her powers, how frequently she acts, and where, and on which organisms and which phenotypes, you ain’t got nothin’, no scientific hypothesis at all.
In other words, not only is evolution true, it also is necessary for proper science. That's convenient.
This argument that strictly naturalistic explanations are mandated in the historical sciences traces back to the nineteenth century before Darwin though, as with several of evolution's metaphysical planks, it gained momentum from Darwin's theory as much as it fueled Darwin's theory in the first place.
Darwin's main concern was that people accept evolution. Which subhypothesis of evolution one accepts, explained Darwin, "signifies extremely little in comparison with the admission that species have descended from other species, and have not been created immutable: for he who admits this as a great truth has a wide field open to him for further inquiry."
Evolution was needed for scientific research as that was yet another spot where creation failed. As he wrote in Origins:
On the ordinary view of the independent creation of each being, we can only say that so it is;—that it has pleased the Creator to construct all the animals and plants in each great class on a uniform plan; but this is not a scientific explanation.
As Darwin’s friend J. D. Hooker put it, if theories of divine creation are "admitted as truths, why there is an end of the whole matter, and it is no use hoping ever to get any rational explanation of origin or dispersion of species—so I hate them."
Thirty years later evolutionist Joseph Le Conte argued that the origins of new species, though obscure and even inexplicable, must have a natural cause. To doubt this, he warned, is to doubt "the validity of reason, and the rational constitution of organic Nature." For Le Conte divine creation was not rational. Evolution, he triumphantly concluded, "is as certain as the law of gravitation. Nay, it is far more certain."
Needless to say this metaphysical sentiment only grew stronger in the twentieth century. Evolutionists, under the guise of science, continued to issue this non scientific mandate for evolution. As Niles Eldredge wrote more recently:
But the Creator obviously could have fashioned each species in any way imaginable. There is no basis for us to make predictions about what we should find when we study animals and plants if we accept the basic creationist position. … the creator could have fashioned each organ system or physiological process (such as digestion) in whatever fashion the Creator pleased.
Felsenstein's metaphysic is nothing new. It falls into well defined clade in the history of evolutionary thought. Of course there is nothing wrong with metaphysics, per se. But let's not pretend we're doing science.