I think I understand your point after having read the links, but it seems to me that scientists must necessarily, at bottom, assume a realist philosophy in all discussions regarding creatures. It seems to me that, in fact, a biologist, when he is writing of "dolphins" in an essay on "dolphin evolution," assumes that the reader will undertand by the term "dolphin" the same thing that the author intends.
Can you give me an example of a case where "pragmatic nominalism" would serve a useful purpose?
To my mind, the use of theoretical models "widely agreed upon by experts" is nominalistic because of the reliance upon "wide agreement" and the acknowledgment that the model doesn't match reality. Of course the incongruence between model and reality can be worked into the Thomistic/realist principle of analogy, but I think it might be an awkward fit.
Or perhaps I've forgotten what nominalism is. I haven't touched the nominalists in years.