I dont think its a matter of someone wanting to ensure a trophy.
The organising bodies for the Nationals and ShelbyFest are, as far as I know, trying to give people a fair go, without fragmenting the competition into too small groups.
My (dim) recollection of the recent ShelbyFest classification was that the 5.0-6.0L group was split with LS and Modular engines being grouped together and older technology (windsor/gen) forming the remaining group.
I think the split of Street/Modified 5.0 Cobras was successful and that this was along the same lines
I'm sure someone will correct me if I'm mistaken here but I believe that the view was that the newer engines were comparitively competitive but - broadly speaking - not really in the same class as earlier generation engines.
I guess where it gets a bit sticky is when people do an extensive rebuild and the inherent characteristics of the engine are no longer there, making the justification for the split a bit tenious.
Personally, I think its a good that organisers try these things out - at the pointy end nobody is complaining that they're competing against 'X' engine type or capacity.
The whole point of grouping similar engines/equipment is to give credit where it is due for set-up and skill on the day.
It doesn't stop anyone comparing results/brands etc.
I guess if the option to nominate into the new engine classification group existed then that would have the effect of denying someones LS a trophy
LoBelly