Mods -can- control those files, actually. I've been doing it with mine. Its obviously not an ideal solution, since the mod maker needs to add each custom ship set in manually or the shipset maker has to add files for each mod.
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Phoenix-D
I am not senile. I just talk to myself because the rest of you don't provide adequate conversation.
-Digger
Just a suggestion... may not be worth anything, but with all the size possiblities already in the game for ships (not discussing bases) maybe the standard should not be so much size but installable features? For example a higher allowance of engines, more armor slots, etc.
Installable number of engines is purely a mod-based feature, not really something that has to do with models. Armor slots, maybe, but your mod can simply use a slot override file if you need to do something fancy and unusual.