The dungeon didn't overflow in the original. Notably because they took out the final boss when it was going to overflow 'soon'tm. And then the higher floors take about 3 days to respawn or so so since the classmates had cleared up to floor 50 or so before Haruka caught up with them and killed the boss they were fighting and then they left. Then they don't have a problem with a dungeon overflowing until a bunch do at once, because generally a overflow is when THE ENTIRE dungeon leaves, including the boss without more respawns. The problem just being that they aren't in the small dungeon and come all at once. Easily enough to flatten a city even if its prepared. The reason to beat the boss then is that it removes the directionality of the horde since it's leading them to attack civilization. If killed the horde scatters and the dungeon loses all power(which it also does once the boss is outside the dungeon.) Where as here it seems like him KILLING the boss unleashed the dungeon when what it should have done is simply turned off the auto-repair and respawn capabilities of the dungeon. (There was a whole thing in the WN where he kept talking about how structurally unstable the dungeon is while skele-lady gets pissed at him because her dungeon is full of holes because he kept going up floors while modeling the dungeon to drop the monsters from the floor above and then killing them while they are reeling from the fall damage. He did that to kill basically everything on the way up.....except the gazer boss. They looked at each other before even entering the boss room and its death gaze bounced off his magic reflection and killed itself.)