These things aren't related. Like, at all. You can absolutely have a strong story to a dungeon despite it being a place where the regular rules are suspended. It's a collapsing demiplane crafted by a long dead wizard. It is the dreaming subconscious of a mad God. It is the ruins of the outpost of a long gone interdimensional technomagical civilization. It is the "mythic underworld" where the laws of fear outweigh the laws of physics. It's Wonderland.Two groups of PCs enter two dungeons. The first group is in a dungeon where things are just raondomly thrown together. Each challenge is fun. However, nothing make sense. The second is in a dungeon that has a storyline behind it and where the DM has made efforts to make sure that the placement of everything works to support that story, and in the ecology of the dungeon.
You don't need to know where the kobolds poop for a dungeon to be compelling and powerful. And chances are, the more real you make it, the more boring the dungeon will be, because every interesting, dramatic thing you might want to do has to pass an arbitrary "realism" test.
Of course, I'm just defending and explaining my point of view. Folks should do what is fun and makes them happy.
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