Tuning can only have a limited effect - the main thing is that the extra cylinder (with the same capacity) has lead to a shorter stroke, which reduces torque and engine braking.
I'd imagine the EMP theory is correct (plus other interesting electromagnetic "weapons").
Interestingly, when the rules were changed a few years back as regarding what is an "Urban Cycle" etc, the Td5 infact came out worse on the Urban Cycle than the 300Tdi - by definition making it worse than the Td5 for emissions, at least on that cycle.
There was to be a "real" Td4 for Defender, but it got canned when BMW decided to balls things up, and I suspect that the oportunity has now gone forever to develop a genuinely approrite engine for Defender.
On the emmissions front, though compliance is tough, I suspect that there is large element of fuel economy factored in by the marketing men that overrules other requirements. I'd hazard a guess that the situation is rather like the "we can't meet regulations to make a new Defender that looks like the existing one" and then Santana prompty launch one.
Richard