I have no idea what the "plug" would be for, and I doubt if there is any real need to remove it.
Can you run a range rod with a proper fitting jag and patch, all the way from the muzzle to the breech-face of each barrel?
If so, she should be good to load and shoot.
I would think that one of the barrels would require an extra long flash-channel to reach the breech of the "bottom" barrel since you say the shotgun is an O/U,.... that might be an area for concern, if you start getting "hang-fires" after a few shots, as I think that would be a likely place for fouling to accumulate.
Just a couple random thoughts, since I've never seen an O/U muzzleloader that wasn't a "swivel-breech".
Another thought,.... is there also a "little plug" along the bottom/rear portion of the stock somewhere,... if so, maybe that little plug in the bottom barrel is for a sling-swivel.