I'm curious, do you have any resources proving this theory about "overpenetration"?
I disagree with your premise that the .40 is better because it "expends all its energy in the game" and that the .308 is worse because it "overpenetrates". Game is killed by the destruction of tissue caused by the bullet. Energy transfer is a secondary, and very minor consideration. The game is not killed by energy transfer, hence your statement earlier about archers.
As we have eliminated the ".308 ball" from consideration, I believe that a .308 hunting round (i.e. some sort of expanding round designed for moderate sized game, like the Remington PSP Core Lokt) will cause greater damage inside deer/hog sized game than a .40 S&W.
http://www.chuckhawks.com/energy_transfer.htm
http://www.rathcoombe.net/sci-tech/b.../wounding.html
http://www.rathcoombe.net/sci-tech/b...ics/myths.html