I agree that having the flintlock in KoK is somewhat convoluted.
I just realized that having the ammo and "accessories" next to the gun seems to hint that it takes place before Predator 2.
If they take it from Harrigan after Predator 2, where would they get the accessories that Naru used? From a museum? Did Greyback give the bullets to Harrigan, and it wasn't shown?