The fast powder's pressure hits the chamber maximum before the bullet has moved much at all. This means the peak pressure is confined to the small volume of the case behind the bullet. The fast powder burns up and the gas that makes that pressure in that small space expands as the bullet goes down the barrel. It just isn't enough gas to be pushing very hard by the time the bullet leaves the muzzle. So, bullet acceleration is mainly during the early part of its travel down the tube.
A slower powder lets the bullet get down the tube an inch or two before the pressure peaks. This means you can use a lot more powder since the peak will occur in the bigger volume that is behind the bullet after it has got that far down the tube. This gas volume then holds maintains higher pressure longer as the bullet goes down the tube and expands the space. This is both because of the larger peak pressure gas volume and because the slow burning powder also keeps adding gas because it hasn't all burned up yet.
Another way to look at it is this: The main propellant is nitrocellulose in both the fast and slow powders. It has the same energy per grain of weight whether it is in a slow or a fast burning formulation or grain shape. The fact the slow powder peaks its pressure after the bullet has moved enough to create a bigger volume behind it lets you use more than two and a half times as many grains of H110 as you can Bullseye. More powder, more energy.
I am curious where you got that 3% figure from? I know W-W used to warn not to reduce 296 loads, but I never picked that up for H110? Hodgdon Manual #27 has almost 10% difference between the starting and maximum loads for a 280 grain bullet in the 44 mag propelled by H110.