Typically what happens is that when a new engine is to be developed [as for the EA288] and/or an existing engine gets an ECU upgrade with new electronic architecture [as for the EA189 with common rail], the fuel injection system supplier [Bosch in this case, but could just as easily be Delphi, Denso or Continental] will supply the new ECU with generic software that has active maps to operate the essentials, i.e. their injection system plus the EGR, VGT and intake throttle [to drive the EGR], and with this the OEM calibration team can begin to develop the base engine in terms of mechanical efficiency, NVH, turbo specification, torque curve, and mechanical robustness etc. Once this has been demonstrated with the development calibration, then work can begin on evolving an emissions compliant calibration that utilizes the full complement of sensors and actuators that are necessary to get any engine and complex aftertreatment to meet the current EPA regulations, including OBD. Getting to this point takes huge resource in manpower and equipment.
Once a robust and durable calibration has been achieved and at a system cost that the vehicle price-point can live with, the emissions map which only covers that portion of the speed/load map the test cycle roams over, is overlaid on the earlier development map and then the outer boundary between the emissions map and the speed/load torque map becomes the off-cycle zone where it is not strictly required to meet emissions - and typically one does not in the interests of conserving urea. This applies to gasoline cars too which often go rich near full load. This off-cycle band is greatly reduced in the US with the EPA '06 cycle, but is still relatively large in Europe. Thus if you are horrified at the thought of "spewing" emissions above and beyond the certified levels, make sure that you never stray into the off-cycle emissions zone.
At this point, the emissions map overlay should be baked into the overall calibration so there is just the one cal, but it rather sounds as if VW did not wipe the underlying performance development map and arranged for it to be switched in again for normal everyday running, but if so then that would be blatant wrongdoing. Nevertheless many in the media are too ready to focus on the "40 X" over the legal limit, but I am confident those are spikes and not steady state values. Also for all we know those values may have been recorded in the off-cycle zone. As I mentioned before, with diesel combustion it is something of a zero sum game since there is a trade off between NOx on one hand and Pm and CO2 on the other. Yes, NOx has gone up some, but fuel consumption and CO2 have come down relative to the legal levels. Ideally we want them all to come down for everyone's benefit.
PJGD