It's clear that the development of the "cheat device" was not the work of rogue engineers; as @sysconfig notes, the people who did it sent letters, etc. So the that shifts the theory onto much firmer ground: who approved which features should be in embedded in which release? And now you have a potential conversation that goes a bit like this:
Engineer (manager): "We've been working on the (configuration of the) emissions control system, and have got much peppier performance/better mileage/cuter boothbabes".
Business unit executive: "Will it pass the emissions tests?"
Engineer (manager): "Yup".
Granted, there's a certain amount of "Thomas a Beckett" going on ("Who will rid me of this turbulent emissions control regime?"), but I don't find it entirely implausible that some manager-of-engineering instructing a minion to leave the "emission test detection" code enabled and NOT reporting that up the chain of command, because he likely would have been engaged in a CYA over the fact that the bloody motor wasn't performing to plan.