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.
That makes sense, but I don't think that this method would serve any useful purpose with regard to creatures, unless there existed a myriad of fossils displaying a continuum of (minute) morphological change, which is clearly not the case.