Oh, I see what you mean, but I read it differently:
A nuke delivers 100-200 EPs, and rolls once for damage. A (let's say) J factor PA spinal delivers 800 EPs, but rolls 10 times in the damage tables, so, each roll is "worth" 80 EPs (40-80% of the nuke's).
IMHO, this represents the nuke exploding on an specific point of the ship, so concentrating the damage effect, while the PA, being a continuous beam, distributing its effect along several points of the ship. ...