I used to work at Chrysler, then Daimler-Chrysler. I can assure you first hand that they are not smart enough to pull something like this off. A friend of mine just quit the emissions lab there a few months ago too. Said it was a complete clusterfuck.
It sounds like they did produce some vehicles that upon further inspection didn't pass emissions. Then when the feds started asking about stuff, it turns out that they didn't do the paperwork right either - that is the part where it talks about them not properly disclosing emissions devices. You wouldn't believe how many little pieces of paper and tubes are all called emissions devices now. Even the air cleaners have emissions devices in them now (activated carbon paper, and PCV). Then you have to pass tailpipe emissions, plus you have to pass emissions after a car shuts off and just sits there. Totally different situations. It is truly a maze of regulations, and diesels are even worse.
This is just incompetence. There is no way that somebody at FCA cooked up a scheme at the VW level to cheat. I could be wrong, like I was wrong about Trump losing to Hillary, but I doubt it!
-Geoff