They are scoring by adding horsepower plus torque and dividing by cubic inches at multiple rpm data points from 2500-6500rpm, then determining an average and multiplying it by 1000.
The "divided by cubic inches" part puts a larger engine at a disadvantage if it can't make equal hp/ci at or near 6500rpm compared to that of to a smaller one. Even if it's more powerful in raw numbers.
To elaborate on this, Let's look at data points at both ends of the scale for a moment.
At 2500 rpm That 371ci made 401ft/lb and 191hp
Giving a calculated score =1.5956
This is one rpm data point to be used for the "average power"
With a 4" stroke, that engine becomes 414ci and is 11.59% larger in displacement, so would have to make 11.59% more the torque and horsepower at a given rpm to achieve the same score.
This is achievable at 2500rpm.
A similarly build 414ci could probably make be made to output 11.59% more torque and horsepower at 2500 rpm.
This would be 447.5ft/lb and 213hp.
Because at this rpm it's not a huge challenge to fill the cylinders, not at either the larger or smaller displacement.
(447ft/lb + 213hp) / 414ci = score of 1.595 points
(401ft/lb + 201hp) / 371ci = score of 1.595 points
Both achievable at 2500rpm..
But at 6500rpm the situation changes.
It's a lot more challenging to get enough airflow to fill the cylinders at this rpm.
The 371 made 403ft/lb and 498hp at 6500rpm.
So (403ft/lb + 498hp) / 371ci = score of 2.4285 points.
The 414ci version would have to make 449.7 and 555.7hp @ 6500RPM to get the same score.
(449.7ft/lb + 555.7hp) / 414ci = score of 2.4285
That's just not gonna happen through the same heads.