The emissions guidelines, in your case, likely weren't being "gamed" so much as the manufacturers were just coming up with innovative and cheap ways of reducing emissions. Start/stop features on some newer cars are a way of doing this but this doesn't sound like someone "gaming" the system. If you're not very automotive savvy then you may have misunderstood what the technician was explaining or the logic/purpose behind the system.
What VW did though is completely different with regards to the software although not necessarily illegal until we have all the facts. Based on what the article says, it sounds like they developed a special "emissions mode" which went outside the normal operating parameters with the ultimate goal of reducing the emissions. That in and of itself is not illegal since it passed emissions that way. The illegal part probably comes from when it switch back into normal mode where it never would have passed emissions that way.
We can assume for one reason or another that the "emissions mode" is unsustainable for regular driving (for one reason or another) which is why it was only used when absolutely necessary to pass emissions.