Yes, I entirely agree that equating natural mechanisms occurring with their being the only thing that can occur is bad. We need to be careful of reversing this argument into “methodological naturalistic arguments are anti-God”. Methodological naturalistic arguments just say “here is what the evidence points towards” they don’t inherently say “this is the philosophical cause”, unlike some people seem to think.
As an example, from personal observation, I can assert that there is a transition from a variety of Yorktown Formation (dated through correlation with fossils from Florida that can be radiometrically dated as mid-Pliocene) species, such as Terebra indenta, Ilyanassa granifera, and Solariorbis yadkinensis; through Waccamaw Formation (dated by the same method as basal Pleistocene) ones, Terebra cf. dislocata, Ilyanassa irrorata and Solariorbis cf. yadkinensis; to recent ones, namely Terebra dislocata, Ilyanassa obsoleta, and Solariorbis blakei. For theological reasons, I believe that God guided this process to produce an amazing variety of species that people like me can now study to find out about earth’s past.