I think it's possible the inletting may be chalked up to wear, maybe some chip out and subsequent smoothing over 200+ years? I don't know. I see what you're indicating but I don't know as though I'm ready to go the 'replacement box' route. I do think the box is original, in fact I think the whole thing is pretty right save the funky games with the lock.
Jim I agree, I suspect strongly that this rifle has a very 'factory' feel to it and was likely made by several employees or apprentices. Quite possibly William Henry never touched it!