We were only given the maximum torque value.
Even so, max torque is obtained at RPM of maximum volumetric cylinder filling efficiency. Upping the engine size from 8.3L To 8.4L brings a 1.2% increase in volume, so at least a 1.2% increase in torque should follow. In fact, the 25 ft-lb gain to 560 was a 4.7% gain. I would say "wow" instead of "only."
The variable valve timing doesn't limit torque, it is probably helping to get more torque (and horsepower.) It is adjusting on the fly to provide better opening and closing timing than a non-adjustable system would allow.
The disparate increase in horsepower and torque is because torque is a measure 'cylinder filling efficiency' and horsepower is 'cylinder filling multiplied by engine speed'. As speed increases, air consumption per revolution is still falling (less torque at higher RPM) but not as fast as before (more horsepower.)
Bluntly, it has to be helping because if you disabled it and left everything else the same, it would lose torque or horsepower somewhere. And having said all this, which sounds like I am correcting you, there are some interesting things you've done and I'm curious about them. Can you describe more of the differences you think exists between your Gen 2 and the new Gen 4? Thanks.