Good read. Thanks for the link. It is interesting to see that (outside of engine design). The main semi-controllable items which they site are injection event timing and gas return design. These seem to be two that we might be able to tackle.
It makes me wonder what the engines look like for those who have an aftermarket tune (non-piggyback). If one of these tunes not only increases power initially but also holds off degradation it could be a major winner.