The timer is almost certainly just there to make up for inadequate instance server capacity as opposed to serving any real purpose. If you can't beat a dungeon in the time alloted, you probably won't be beating it even if you take another 6 hours anyway so it's not like it's actually stopping people from winning, because anyone who would run out of time probably isn't winning to begin with. It's also irriating when queue up for 20 minutes and joined a dungeon that has 10 minutes left before expiring.