The reasons to tune any engine diesel or petrol are exactly the same. You want the engine to be more efficient and or recalibrated to suit the modifications you have made. You may want better fuel consumption and torque for towing. You may have made modifications. A larger exhaust better intercooler or as advanced as a replacement turbo and injectors
We will talk more about the modified aspect of tuning but the principal for optimising the tune is the same for modified or unmodified. Let’s get the whole stage one, two and three tunes explained first. Stage one is for an unmodified vehicle, Stage two refers to a tune performed on a vehicle with basic bolt on mods. Mods like exhaust and intercooler. Stage three is for more serious mods including aftermarket turbos and larger injectors.
All the modern diesel engine I can think of use a turbocharger to add air flow into the engine. A large number of these turbos are a VGT (Variable geometry turbo) these turbos control turbo boost by the angle of the vanes directing exhaust gas onto the turbine wheel. The angle and operation of the turbo vanes is an aspect that can also be tuned. More boost equals more air flow into the engine.
Larger exhaust systems allow the exhaust to flow more freely out of the engine. Allowing the new fresh air to enter the engine with greater ease.
With diesel and GDI engines allowing some of the air to exit through the exhaust is not an issue. It is most definitely an issue for petrol port injected engines but that is a topic for another day.
Throttle blades are fitted to many modern diesels. They are really only used for the EGR and for smooth shut down.
EGR and DPF are of interest to many. EGR has the potential to cause two issues. The first is the well know soot deposits in the inlet manifold. This soot needs to be regularly cleared out by induction clearing or physically removing the manifold and cleaning. The second not as well know issue is cooling leaking into the EGR cooler. These coolant leaks will cause a simple overheat all the way up to a catastrophic engine failure.
DPF is a filter for removing soot from the exhaust. A DPF is a large restriction to exhaust flow, as we all know any restriction to exhaust flow reduces air flow into the engine which impacts on the potential for power production. Both DPF and EGR are emission control devices. Being only for emission control both of these can be deleted or removed. As well as physically being removed the tune file has to be modified to prevent engine codes and limp mode being activated.