"If the theory of evolution is not correct, on the other hand, then such orderly change is not expected." [George Johnson and Jonathan Losos, The Living World, Fifth Edition, McGraw Hill, 2008, p. 296.]
How can we know, Hunter asks, that only evolutionary theory can explain orderly faunal succession in the fossil record? Now, that's not quite what Johnson and Losos say; their point is that of the theories (and substitutes for theories) that actually exist to inform our expectations, none would lead us to expect, e.g. that we would find fossils of Tiktaalik rather than fossils of Ichthyosaurus or Rodhocetus in Devonian sediments. If species (or genera, or even families) originated separately, underwent only "evolution within kinds" and were unrelated to one another, why should we find that recent rocks contain many extant species, while somewhat older rocks contain few living species but many extinct species in extant genera, and yet older rocks contain even fewer extant species and genera, but extinct species that clearly belong to modern families and orders, and so forth?
One can posit, of course, that the Designer designed and made them that way, but such a pattern doesn't follow necessarily from design; one would not expect to find such a pattern of faunal succession. Independent design and creation does not forbid such a pattern, but it certainly doesn't require or provide any incentive for it.
I don't see, either, how evolution without common descent (separate origins of lineages that evolve indefinitely without branching much), as proposed by Lamarck in the early 19th century and Senapathy in the late 20th, explains the pattern either. I can't think of any cause other than branching descent with modification that would produce such a pattern ... which is all that Johnson and Losos are saying.
What Dr. Hunter calls a metaphysical prejudice is in fact an epistemological preference: the view that the best explanations are the ones that actually explain things. A theory of origins in which orderly faunal succession is an expected consequence is thus preferable to theories in which it is possible by coincidence but, indeed, not expected for any reason that follows from the theory itself.