Here's my best take on this whole thing:
Let's say we have two handgun rounds. Let's also make the following assumptions:
- One is FMJ
- One is JHP
- FMJ will penetrate completely through the target
- JHP will stay in the target, but penetrate enough to hit organs
- The bullets have the same mass
- The bullets travel at the same velocity
So, the two rounds will have the same energy, but the FMJ will not transfer all of its energy to the target. Since energy is required to do work, which in our case means tear tissue, the more energy used, the better. If tissue is acted on with a tensile force that exceeds its yield point, it will be damaged. Tissue is very elastic, so the energy necessary may be the same as that to actually tear it. It is important to know that for materials, including tissue, energy is consumed by deformation, and can be approximated by the area under its respective stress-strain curve.
Now, the clear problem with the comparison is projectile size after impact. Because the projectile would continue through the target, the excess kinetic energy/momentum must be transferred in full before stopping in the target. the simplest way to do this is increase the cross-section size in the direction of travel, giving more surface area for the energy to transfer. The increased area of transfer allows the projectile to damage more tissue along the path, resulting in a more effective round, assuming sufficient penetration. This also reduces the stress (by increase of area, since stress is force divided by area) on the tissue ahead of the round, halting the round sooner. This increase in area may also sacrifice the last bit of energy, since the tissue at the very end of the wound channel can elastically absorb more energy without breaking if there is more area.
Because of the relative size, let's ignore momentum as a big contributor to damage, and look at kinetic energy. Momentum is an important underlying concept, as the bullet will stay in motion until acted on by external forces - resistance of the tissue to deformation. The bullet will have two forms of significant kinetic energy - one from velocity, one from rotation. The former will be larger than the latter. As stated earlier, this energy, in the JHP, must be completely transferred if it is to stop. Thus, more work has been done inside of the target. The only situation in which a more direct comparison could be made is if the JHP hit something while in the body (bone, maybe?) and stopped. If it was suddenly stopped in the target, the remaining energy will be transferred, possibly resulting in another fracture.
The problem with this discussion is that there is no real way to compare two rounds of identical energy, mass, and velocity hitting identical targets, but transferring drastically different amounts of energy. The best we can do is understand that penetration and hole size are the main factors in the wound, and that it consumes energy to make that hole. No momentum/inertia, no hole. No energy, no hole.