That was interesting reading. It's hard to argue with empirical testing. If I were to hazard a casual guess, I would have gone with the full bore tube as producing a higher velocity. My rationale would have been that the expanding gas has a greater distance to act upon the projectile. Live and learn.
Also of interest that someone actually still uses a ballistic pendulum. The last one I saw was the one I built in 1964.
Thanks for the interesting link Tim.