There are other differences here too, I think. The water heater trick is passive manipulation that stays in place at all times, which limits how far from "real" performance it can get. And per the story, it seems more like "teaching to the test" than "cheating". That is, Volkswagen consciously moved away from the mandate outside of testing. The water heater was (potentially) as energy-efficient as they could design, with the test score manipulated on top of that.
None of that makes it harmless - if "as good as you can make" doesn't hit standards without manipulating them, that's still a problem. But I do find it less galling than "intentionally worsens emissions outside the test bench".