Type of drill bit used, square vs rounded corners and size are three things to consider.
Maybe the Tool Collectors can answer when the modern bit came into use, i.e. the bit with the little screw point lead. For an early gun I'd use a Forstner bit to rough out, then finish with hand tools to cover up your machine work.
Four old guns I examined were:
1. Attributed John Haga, Lancaster County, daisey head patchbox. 11/16" deep x 1-1/8 wide x 3-1/4" long. NO bit holes showing, he used the older style bit to rough out. All four corners square.
2. Attributed Shroyer, York County. 15/16" deep, 3/4" wide x 3-5/8" long. Bit holes show. Front end of box square, butt end somewhat rounded.
3. Henry Deringer. 9/16" deep, 7/8" wide x 3" long. Bit holes all show. Butt end of box full round, i.e. same radius as bit used to rough out.
4. Late flint rifle, location unknown: 9/16" deep, 5/8 x 2" long, both ends full round, bit holes show. 2" long cavity considerably smaller than lid.