Actually, I can easily see that happening. Some poor software guys are under immense pressure (no diesel pun intended) to get this new engine the board loves to meet the requirements. Late one night one says to the other, "Hey, why don't we just hack the emissions test for now, and we'll fix it later because there's lots of time before we actually ship!". So they do, and they report to their manager they've finally gotten it to work. The manager isn't technical enough to know they're BSing, and he reports up the chain the new engine is a go. They meet the ship date, everyone is happy. And it all starts to snowball from there. Marketing spins up, everyone believes the test results (and why shouldn't they?), maybe even the software guys get a bonus, promotion, or technical award for meeting the tough challenge of decent emissions and good power and good economy. The company starts using that engine everywhere, because on paper it's better than all the others. No one realizes it's just a hack. And it never does get fixed.
It really does seem plausible to me that the hack really did originate with some engineers and management wasn't aware of it for quite some time, if ever.