It could easily be a really deep rabbit hole. I am not an automotive engineer but I do work for an auto manufacturer. Just developing their internal financial software. From what the article says, some device was throttling the emissions, triggered by embedded software. That involves fabrication, tooling, etc, etc. The current CEO probably legitimately had no idea, you're right. But various lead engineers, software designers and quality assurance people might have been questioning the changes (that were probably either done at last minute after all control checks were completed and production was greenlighted, or at design level from the very beginning. But few people knowing their actual purpose).
But if we find out their lobbyist groups and shit were intentionally trying to keep these "solid tests" in place its going to be an absolute circus. VW is going to have to answer some really hard questions and I am actually extremely curious how much of the investigative results the public will get. A lot of people had to know about it along the design/production chain for it to work.