The "emissions cheat" in question altered the output of the car when it was being tested. So, they were testing the emissions that came out of the car.
"EPA regulators said that Volkswagen adopted a 'sophisticated' algorithm that turned on vehicles' full emissions controls when it detected they were being tested for emissions performance." - http://www.usatoday.com/story/money/cars/2015/09/18/epa-accu...