One advantage for heavy over light:
Less inputs
Also, testing in sandbox seems to give you a miniscule time advantage for heavy melee (standing next to the machine, you end up killing it at the beginning of the 7s, while light finishes more towards the end of the 7s from what I see, probably due to the fewer inputs).
As for bad game design... it encourages people to do heavy melee attacks. When you hear the repeated sound of heavy melee around them you can pretty easily deduce that someone is interacting with the machines. But it doesn't force people to do so, unlike the rejuvenator, so people can decide how they interact with it, mix it up and . In fact, the damage being a flat 40 that you can't circumvent is mentioned in the FAQ guide (which is written by a moderator). If this was unintended it would probably been fixed already.