Any idea why two lvl 49 Protuberances would differ so drastically?
Played any coop recently?
If I’m not mistaken there was a bug noted when people joined game at different level in cooperation mode.
Only the item card was affected and not the gun per say.
Maybe test it on the field (Or on a vehicle you can spawn on Santuary III) to confirm both guns damage output.
No COOP ever.
And it’s not just item card. I did field test them, and the weaker one performs like a level 20 gun whereas the other one shots weaker fleshy enemies (and that is without using the anoint)
Strange. 
I’ve encountered the same exact problem. I think the dmg rolls are just that vast. Found first purple protuberance and it had 300dmg, later on bought one from Marcus that had 1600 dmg. Come to think of it, the best protuberances I got have always been from Marcus or Earl. Never a found one. The ones I find always have low dmg
Look at the mag and see if it has a +600% or something bonus. I got a level 49 one today with a mag like that that was better than every level 50 purple I’ve found and the mag was causing it. I’m not sure what they did when they nerfed them but there seems to be a lot of variation in terms of damage between different versions.
Yes, its the magazine part that adds +620% damage and +300 splash damage radius. The different magazine types with this large damage gap exist since release.
The nerf from the very first hotfix reduced the damage by -65% and the DoT damage by -85%. Before the hotfix these weapons did up to 10k damage per shot and 20k DoT damage.
See here for screenshots I posted some weeks ago:
