I'm pretty sure that was a commercial, factory-made barrel and was very likely never a flintlock.
If you look at the muzzle you can see a circular line where it was lathe dressed and likely held on an arbor and spindle while the flats were dressed.
My guess is the barrel was made post 1850, possibly even post Civil War.
The cup around the nipple was, as someone suggested, a shield. It directed blast and pieces of the cup up and away from the shooter or someone standing beside him.
The style of the stock and furniture also suggests post 1850.