a) an underground city (your analysis is spot on, doesn't look like that)
b) a cave system
c) a mine
d) a prison
e) the lair of some non-intelligent species
f) a fortress to protect something
Another option is that they're supposed to be 'abstract challenge spaces' (as another commenter claims), but roguelikes aren't intentionally abstract: they attempt verisimilitude on lots of levels. Nethack in particular has a very detailed naive physics with all kinds of internal logic.
Brogue does its natural caves pretty well, I think. Minecraft seems to, and places its seams of minerals reasonably (neither are perfect, but they're clearly trying).
But this kind of dungeon generator? We're nearly 20 years after Crimes Against Mimesis [1] was written, and this feels like a big step backwards.
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