Rob Sheldon notes, in response to this post, and our discussion of MN in general,
Methodological naturalism works great on superstition and animism. It evolved as a response to the inborn nature of humans to “wear the lucky blue sock”. But it prevents the doing of good science, as you point out, because it cannot question its own presuppositions. Therefore it is a “vestige” of formerly useful organs, a “living fossil” of what is no longer viable.