There's a bit of a difference between 'muggles as setting elements that an author has decided are less relevant' and the sense of the word as used in the original question of this thread, which was more about mundane versus magical methods of accomplishing things. Of course, if we go so far as to talk about entities in a fictional setting which the author has specifically decided not to tell stories about, then those elements can never be relevant in that setting. So we have Watchmen where figures like Rorschach, the Comedian, Ozymandias, etc are always at the center of events which change the world as opposed to, say, a widespread grassroots protest movement or the full force of a foreign government. In Harry Potter, muggles aren't relevant specifically because it's not a story about muggles, and yet at the same time it's a story written by an author, who makes a conscious choice as to the subject matter.

But that's very different than the sense of the word used to divide supernatural elements of a setting (or character) from elements that have direct real world correspondences (the so-called mundane elements). A wizard who is very wise has both supernatural elements (their magic) and natural elements (their wisdom). The killbot example I gave was to create a case in which something only had its supernatural advantages, but all natural advantages were removed - a counterfactual, in order to see whether the factor determining its impact had more to do with the powers themselves, or the way in which they were intelligently applied. In the end, if the killbot has to understand humanity and modern society well enough to for example target oil refineries, then for me at least that story is more about the strategy of dismantling society by attacking the oil than it is a story about how this guy can kill things within 30ft. At that point uou could replace the killbot with a terrorist organization or a foreign military and you wouldn't lose anything from the meaningful bits of the story.