I agree that the analogy doesn't hold for the recent VW debacle (where the calibration was changed during certification testing), but it holds for the industry in large and what has been going on for the past 10-20 years, which is what the paper is about.

The vehicle manufacturers optimize the engine calibration to the drive cycle they are trying to beat. That is why a US-spec BMW has a different engine tune than a Euro-spec BMW for example, the drive cycles are different.