Okay, let me ask this....
If a 405 grain bullet from say a 45-70 is going a mild 1000fps and does not make it through a deer, well no that is hardly possible, lets say does not make it through an elk but stops short of the ribs on the far side. It has expended whatever energy a projectile of 405 grains at 1000 fps has to offer right?
Now, if that same bullet were going say 1900 fps and blew through that elk but used only the energy of a bullet going say 1600 fps to get through the elk and the last 300fps of energy was "wasted" in a tree or in the dirt would you say that the first bullet imparted more energy to the elk than the second? NO! For that matter, if you could make that bullet go 2100 fps it would impart more energy to the elk than the one going 1900 simply due to more energy available. It's not just about pass through or no pass through. It's also about how FAST it goes through, how much resistance it encounters, how fast it decelerates and how much disruption it causes in the time it is passing through. You'd have to get pretty deep into the physics of what is going on to really figure it out.
The only way complete penetration means less energy transfer than a pass through is if you are shooting the same bullet at the same speed but hit different stuff in the critter. Take two 1600 fps 405 grain bullets that both hit an elk in the chest but one catches both shoulder bones square and does not exit while the other hits nothing but a rib on one side blows on through. That would be an example of a pass through transmitting less energy than a bullet staying in the animal but it is due to an adequate load encountering maximum resistance. If you start changing speed or bullet weight and getting velocity up there a bit higher, you're gonna do a whole lot more damage even if the bullets pass through every time. Loading down so that a bullet stays in the critter on purpose is simply reducing available power and to me is totally pointless. Now, if you are talking about little bullets like a 223, 243, 22-250 etc blowing up and not exiting then yes it is effective because there is so much energy there and there is massive disruption in the bullet path. But with a 45-70??? Doesn't really apply. That heavy, slow bullet is in a whole different league.