The NYT is not at all confused. The cars in question have software in the ECM specifically meant to detect testing. The software looks at various inputs, including steering wheel position, speed, duration of operation, and barometric pressure. The values it looks for precisely track the parameters of the federal test procedure use for EPA certification.
When the software detected this, it switched to a mode that VW actually called "dyno calibration". At all other times, it used a mode VW called "road calibration".
Source: http://www3.epa.gov/otaq/cert/documents/vw-nov-caa-09-18-15....