There are a number of things that can increase, or DECREASE efficiency of a modified diesel at part power: timing, puming efficiency of the heads, pumping efficiency of BOTH SIDES of the turbo, exhaust flow and fuel atomisation.
It depends on where on each of those curves the OEM was at that particular RPM/fuel feed combination, and where the modifier puts those components after the fact.
Timing is self explanatory. It is either ideal or more or less than ideal. IMHO, OEMs never err on the "more" side when it comes to leading initiation of first phase of combustion. I believe one thing that Giles mentions regarding his mods is that he changes the dynamic timing. This is a lot easier for a chip tuner than someone doing mechanical work, but I believe that is one HUGE area for improvement - especially on pre-emission engines.
Efficiency of flow at the head is dependant upon the pressure differential available to make the air move, and the ability of the port/valve/manifold to move it at that velocity. As flow velocity increases, pressure drop (and the energy needed to move the air, as well as the mass of air actually entering the cylinder) drops of exponentially with flow velocity (= RPM). That is why at the end of the day, an NA drops off badly with revs and will smoke (thus the "traditional" habit of pump designers to defuel at the higher end of the rev band of a high-speed engine). All of that pumping stuff takes HP, costs available air....
BUT...it inversely the case for turbos running in the sweet spot of the either or both turbine maps. This is why a turbo can cover up a lot of weakness in head design..for PART of the rev band. Thus, mods to the whole shooting works will only deliver where the flow of each gas-moving component is ideal (thus giving more power due to the available energy moving more air - and due to less parasitic loss due to doing so more efficiently). The bottom line is you need to get the exhaust turbine and housing right for the flow on that side (at the desired RPM/EGT) and you need to get the compressor housing and wheel right for the same reason. Add to that the manifold and head porting - which are a total loss REGARDLESS of what method of induction is used, so need to be as efficient as possible in any case) and you can see that a modified engine may be at an very efficient, or even INefficient mode at cruising RPM.
Finally the poop chute: Constipation is good for no engine, and diesels will benefit from the same mods here as gassers. EVERY NA should have a nice header and free flow exhaust system for efficiency and power, and every turbo should have as much downpipe and tailpipe flow as it can get to increase exhaust turbine efficiency and decrease EGT.
Fuel atomisation is the dark horse. One of the things that makes modern diesels as clean and powerful as they have become is the drastic increase in injection pressure - which results in much better fuel atomisation. One of the risks of higher flow injectors is running into pump pressure limits (i.e. can't be maintained dumping through the bigger holes) which can cost efficiency and emissions.
These things are mostly "free" power (when it comes to displacement and fuel used - if not out-of-pocket capital cost). But you can see, for most factors that effect power they similarly improve efficiency - but only within some limits. Doing one will often compliment the other, but slipping over the edge of a flow map or pressure limit can give more of one at the expense of the other.
Sorry for the lengthy answer, but as Giles will tell you, I am kind of hung up on getting the details right.