"DEF (Diesel Exhaust Fluid) is used as part of the SCR (Selective Catalytic Reduction) system, where the urea-based DEF is used to aid in the 'breaking down' of oxides of nitrogen (NOx) that are a major combustion byproduct of the diesel compression-ignition process.
High levels of NOx are generally created by high in-cylinder flame front temperatures, a side effect of high cylinder pressure which is most common under high load (high power). When we tune an engine, we're always watching NOx (as well as HC, CO, and CO2) emissions, and we often times will find that there is a finite limit to the extra power that can be created without substantially increasing the emissions. Careful handling (not shutting off, but proper calibration for higher output) of the turbocharger, EGR, and injection control systems allows us to make more power cleanly, without requiring a much higher rate of urea injection to compensate for increased emissions."
I think the gist of it is if done properly you can still get performace and mileage gains with the emissions equipment in place. It just takes more time, patience, and knowledge. I hope this answers your question.
2014 Jeep Grand Cherokee 3.0 diesel -PPEI DPF/SCR delete tune, Custom 3" down pipe, BANKS Exhaust