I have a couple of questions and /or observations.
The box--
I think this may be the original box in which the rifle was sent to your ancestor. The box is sturdy enough to survive shipment via rail or wagon. It looks like at one time there may have been a paper attached to the inside of the lid-perhaps an invoice or packing list was there? At each end of the box, there's an extra block of wood-are there screws in these block that maybe were used to hold down the barrel and stock of the rifle? I see were the extra block on the left side of the box has a concave cut in it-could that have been used to hold down the stock? Then there is the section of the box where the false muzzle and plunger would have been placed for shipment. And there's a wood screw on the lid of the box- clearly if this was a box for storing shooting accessories, there wouldn't be a wood screw there but some type of latch. I know you said that the box is too short for the rifle. I don't think so, and I'll explain that below.
The rifle-
It appears to me that the barrel can be removed from the rifle-
From your picture, at the breach end of the barrel, you can clearly see a line that runs around the end of the barrel (it actually cuts through the part of the bolster that surrounds the nipple). There is also a tab that extends from the lock face into the breach face to keep everything aligned and secured. You can also see what looks like the end of a bolt which passes through the breach face. My theory is that the breach plug, which is at the end of the barrel, has a tang that extends from it and that fits into the breach face, and the bolt I referred to above holds the barrel tight against the breach face. By removing the bolt, one could remove the barrel from the action-in effect, it become a take down rifle (the action become separated from the barrel), and therefore it could fit into the box, i.e. the shipping container. A lot of modern muzzle loading rifles have a type of hooked breach system which allows the barrel to be removed from the action- why not this one? The barrel could be removed for cleaning or to put a different barrel on the action.
Could you supply a couple of pictures of the left side of the rifle around the breach face area? I'm interested in what the end of the bolt looks like from the left side of the rifle. The bolt would have to securely lock the barrel up to the breach face, so there would be no barrel movement.