The Lyman 48 sight required inletting into the stock which that stock does not have. If by some strange quirk the buyer requested the receiver be drilled and tapped for the sight but did not have SA install the sight, this might explain the holes. Unless the Sales letter noted this, I would expect that the holes are a later addition. I believe it was Lyman that made a post WWII sight for the 1903 that did not require inletting into the stock.
The rifle is a beautiful NM, but unless verified as original, the holes do affect the value somewhat.
Forgot to add: usmartialarmscollector.com/