A simplistic answer
Yes if the engine does not each operating temperature then the ECM calibrations will effect the NOX readings. I have done a number of dyno runs with the 4.0 based engines and they like heat. Power output at 200 degrees vs. 210 shows an increase in efficiency at the higher temperature. Stock these engines came from the factory with 195 thermostats. Running anything less will lower performance and increase emissions.
On my stroker (equipped with a 195 stat) and an electric fan the engine temperature would cycle from 210 down to 180. The ECM was constanly trying to re-adjust for the temperature swing. Changing back to a stock fan, clutch and shroud coupled with a Hesco brass 3 row radiator has the engine running at a steady 180. Whether in traffic or on the freeway. The ECM is now in a steady mode compared to what it used to be and the engine runs much better. My only compliant is that it now runs a little to cool. I`s like to see another 20 to 30 degrees to optimize the calibrations.