pomofo,
I agree with miller about proofing in the early days of nitro powder. Early barrels were proofed before bundling them together, this was the provisional proof. It was done this way, so less work would be lost if the barrels failed. The proof after assembly is the Definitive Proof. Absent the crown R, the barrel wasn't rebored, then. You might be right about a die slipping. The "polished out" mark may be one of the workers marks. There are three common "Gauge" marks used on pre 1911 9.3 rifles; 118,35-108,49- and 99,70. The 108,49 as found on your rifle seems to be the most common and usually equates to a barrel with about .362-.364" groove diameter. If you "slug" the barrel you should be able to measure it( be careful of odd number of grooves).
Mike