I am with you, it does not look right. Parashooter has been most helpful with the drawings and reality checks.
The rebuilds done by the arsenal resulted in a lot of parts being mixed on these old Krags. There might have been slight changes in the details on the screws and sights over time and parts were taken out of bins on the rebuilds and assembled with next part picked up. There is a real possibility these were just made that way, the screw head sticking out is not in a place were it would hang on things or cut an operators hands on a mangled slot.
The drawings used in the manuals were not done on CAD but by hand, so the proportions of the manual drawing and you your actual screws being different may mean nothing as the drawing is done by hand. I make drawings in CAD for CNC programing, then wipe out the numerical tags and add tolerances for actual running production. I will take the same drawing and remove the numbers again and rescale to metric for a technical drawing for a customer, all proportion in the drawing will stay the same in all the incarnations. Not so in the old days.
Another possibility is someone ran a couple of days production on a machine with too thick a head. Human nature being what it is we hate throwing stuff away. One or 2 parts discrepant while setting up a machine and I will toss them instead of messing with them. A couple of days worth of production and you ask if it will hurt anything if we use them. I read an account where a operator at Ruger cut a 1000 barrels and inch short. They became the basis for a short run of specials that collectors look for now.