The point of a bong is so that the smoke will be filtered slightly/cooled by the water/ice/other fluid that you have in there. For this to be accomplished, the smoke has to go from bowl > stem > water > chamber > mouth. If it's out of the water, then you will not get the benefit of water, and then you're basically just smoking a fancy pipe. The longer distance that the smoke has to travel through the water (or ice, or other liquid), the more filtering/cooling you get.