I was thinking there might not be as much energy transfer with pass throughs.
There is
plenty of "energy transfer" with pass-throughs. It's not like the bullet is a scalpel, making a clean gentle slice, or a drill making a nice clean hole. It still
slams into the animal. I'm sure you are familiar with temporary wound cavities and such (the huge gourd shaped hole that is created from bullet impact). You get that from any hit, whether the bullet remains in the animal or passes through. That is where the majority of your energy is transferred.
With your line of thinking (wanting the bullet to stay inside), you have one hole. What if the fat or hide shifts over it, and blocks the blood trail? How deep did the bullet penetrate? One lung? Two? Heart as well? Maybe the liver if an angled shot? Maybe, maybe not. You're never sure until after recovering the animal.
With a bullet designed for and capable of pass-throughs, you know what you hit.... everything between this side and the far side. You deflate
both lungs, and open up an extra air leak to the outside on both sides, further guaranteeing that both lungs collapse/fail. Ain't no bear, elk, or anything else going far missing both lungs, though they can travel surprisingly far with just one out of commission.
With that pass-through shot, if one hole gets clogged up with fat/tissue/hide, you still have another for blood to make it out and to the ground, aiding in your tracking job. Besides, the second hole is usually larger than the entry, thanks to expansion, offering an even bigger benefit.
I can't think of too many advantages to a bullet that stays inside the animal, versus one that punches all the way through. I will
gladly dump some of that "energy" into the hillside beyond, in exchange for the above listed advantages.