If the design requirements state: "engine must meet emissions during test" and the tests show this to be the case, how do the compliance department argue otherwise?
The compliance departement is supposed to test independantly for exactly the same reason you software testers should actually test the product and not just believe the software engineer when he says: "it works".
Part of the job of the compliance department will be to write the requirements that ensure the design and engineering teams build something that's actually legal to drive around on the road. If they wrote a requirement than "engine must meet emissions during test" then they have failed to do their job properly because there's a very obvious flaw in that requirement.
IMHO that does not matter. If they knew about the software, they are the ones responsible, not the engineers. And it seems unthinkable that engineering just went ahead and put in the software hack, without getting a go from management or the compliance dept. It's about who signed this off.
The rules say you can't use a defeat device and operate differently during the test.