Yes. In the Lucky Gunner testing of HP .38 ammo, they test the same ammo from 2" and 4" revolvers. It's not at all uncommon to get more penetration at a lower velocity from the 2" barrel. The explanation there is that the bullets are expanding less at lower velocities and so they penetrate deeper -- very like the flattening of the higher velocity soft lead round balls in the black powder example you cited.
In the case of the two projectile loads, I suspect that the explanation for deeper penetration than predicted is some sort of "drafting" effect.
Some time ago, 35remington suggested gel testing a single light wadcutter at the same velocity as the two projectile loads to see if the equations actually work for a single projectile. That's a good idea. I've just been too lazy to work up single projectile loads that match the velocity of the two projectile loads.
My current "hypothesis" for the extra penetration of the light projectiles in the two projectile loads is that even though they punch two separate wound channels through the gel, for much of their paths, they only create a single temporary cavity. I have no idea how much bullet energy goes into creating the temporary cavity. But the gel is surprisingly tough stuff and there has to be some work involved in creating that cavity. So if two bullets can share that work between them, they'll have more energy left for the productive work of punching a deeper permanent cavity. It makes sense to me. But I don't know how to quantify it or "prove" it.
At any rate, I just realized that I didn't post the temporary cavity pics (such as they are) for all five shots from the last gel test.