The dev team has shown with Aquapolis (and to a lesser extent Deep Dungeon) that they're willing to throw lore out the window for the sake of content. I think they gave one throw away line about an eccentric adventure who hid maps around the realm, but if Koji tried to explain in detail why treasure chests open portals to hundreds of dungeons each with their own sets of caged monsters (who feeds them?) that have been down there for years, presumably, he'd have a heart attack.

Palace of the Dead technically has lore reasons behind it, but for the most part