I'm stealing my colleague's response:
Basically, we are erring on the safe side. We have seen and heard of many premature burnouts for the pump when used externally. Naturally, the pump is going to run cooler when submersed since water is a much better conductor of heat/cold than air. Also, we have seen external seals wearing out over time. Used submersed, that is not such a big issue as the water will leak into water. Used externally, the user would need to silicone and waterproof the unit when the leaking starts or replace the pump.
That said, the mag drive pumps are an excellent pump and a great many of our customer use them externally with good results. We just want our customers make an informed decision.