A gun should do the same damage as another gun given it’s setup the same.
A coachman with the same mods as another coachman should do the same damage.
But make it “Rarer” and suddenly it does more damage? How?
The receivers in Fo4, I could forgive for game-play purposes, maybe you could reload your brass with more powder or whatever, but the rarity system just doesn’t make sense, and honestly pisses me off.
In fantasy settings the traditional explanation for this is “magic” (i.e. the reason an axe+2 can do more damage than an identical plain axe), and people have learned to just accept this. Maybe it’s best to imagine the answer is “nanobots”.
Nanomachines, son.