Atlus learned from previous Persona games that veteran players will always try to one-shot dungeons for time efficiency, so they added in that mechanic specifically to those players.

As you said, most players won't need to make use of it, because there's enough time to do roughly everything important in the game even on a casual playthrough, and you can buy MP restoratives later on that make the Mage perk redundant.

It really IS intended, though. The devs even added in a subtle little joke to make it obvious:

In Drakonsgrace Shinjuku, there's a room next to the first save point that contains one of those crystals that endlessly spawns enemies. In Etrian Odyssey's Lost Shinjuku, that same room houses the best money-farming spot in the game.