In the design they used, the exhaust needed to be on the bottom so that any condensation doesn't drip over the intake or get sucked into the intake stream and potentially clog it with ice on a super cold day. Also note that the condensation collection is only on the exhaust, so excessive moisture on the intake would be going through the gas valve and venturi, potentially messing that up as well. It was clear in the installation manual, but they didn't follow it. How the thing is designed will dictate the orientation. Many concentric ones probably are immune, but still follow the instructions!
Some plastic ones I've seen used have TOP molded into the housing, that should make things clear. Mine is all metal (SS). They also show some plastic ones that will work, but it came with the metal one.