I agree that gameplay-wise shuffling into the deck is better. Otherwise, becoming good at the game means having to memorise the positions of all the cards you have escaped! I'm not sure I find that fun :D
From a narrative point of view, I don't find it a problem - you could say that monsters are roaming. In any case, 'put at bottom of deck' doesn't ensure you get the same rooms, since you don't always escape a full room. So the current narrative of "returning to the same room" is sort of broken already.