Raimey,
The Mod 46 commercial and 94 military were the same action made on the same equipment. The difference would be in the markings (and stock, of course). The barrel would have commercial markings on the mod. 46 and the military rifle would have a military crest on the receiver and other marks on the side wall. If someone took a military action, put a commercial barrel and stock on it and cleaned off the military markings, it would be difficult to tell the difference. BTW, I bought my very first drilling from a gunshop in Selma. That would have been in 1964 or 5, you were just a baby then.
Your rifle has at least two sets of scope mounts installed over the years. One set had two bases with two screws each, maybe Weaver. The other one was a one piece with two screws in the receiver ring and one in the bridge, possibly a Readfield.
If the holes were properly drilled and tapped, there shouldn't be any concern. The typical size of the screws would be 6-48 but a few people would open up the holes in the bases for 8-40 screws, usually for heavy recoiling rifles.
Mike