Ok, that explains how they get the Weapon Damage Bonus, and the math checks out when I run it, so it is nice to know the stat screen is right with the bonus percent.
What it doesn't explain is why higher firepower is resulting in lower damage per bullet for a lot of guns vs. the same variant/level/mods/stats gun with lower firepower.
Two Pistols for example:
Pistol 1 works out to 4387 damage per shot, and Pistol 2 works out to 4702 per shot despite being lower firepower. Both natural 50 drops on the same variant, no mods that change firepower.