Most of the discussion about that post has focused on roguelike computer games, so I didn't want to clutter it up with a discussion about the more general point, which Jeff puts as:
D&D was designed for dungeons. Sounds obvious, I know. But hear me out. D&D was not designed for ecologically-sound underground lairs. D&D was not designed for adventures with plots and stuff that happen to be set at least partially in subterranean labyrinths. You can do both those things with D&D, but the game is ideally designed for the big, sprawling megadungeon where Orcus lives on level 20 or whatever.
These sorts of dungeons are often considered fairly hack-and-slash oriented (not necessarily bad), but Jeff points out that this isn't necessarily so:
...built into the scenarios is the assumption that the party doesn't just show up to the dungeon and wander willy-nilly. Superior dungeoneers reconnoiter. They map. They plan. They interrogate or charm monsters to get information. Certainly you can slop your way through a dungeon crawl if you want (and that can be lots of fun) but if you want to do a good job of plundering the dungeon you take planning and reconnaisance seriously.The problem here is that these two quotes aren't wholly compatible.
If I'm doing investigation in order to learn more about the dungeon, I'm going to want to use that information. If I plan based on that information, it had better be coherent. To me, that includes some semblance of an ecology. For instance, unless there's some weird stuff going on (which there might be), things living in a dungeon need food. Attempting to starve out - or poison - things in a dungeon should occasionally be a valid (if not necessarily effective) tactic. It also includes some sort of society. Things living in the dungeon - if they know about each other - will have opinions about each other and relationships (even relationships based on fear are relationships) that can be manipulated.
If superior dungeoneers do a really good job at information-gathering and are really clever, do they force the megadungeon to become a thing of intricate social and ecological detail? Are dungeoneers supposed to do merely a mediocre job at such things so as to not break the megadungeon assumptions?
There seems to be a slippery slope here... and I suspect t leads to somewhere other than dungeon level 20.