It might only affect the looks of your rifle honestly. If there are all the right washers in there with the bolt then I can't see why there would be much issue with the square not protruding as far. Only reason it has the square is to stop the bolt coming loose in harsh environments like war, which I suppose you don't plan to join with that rifle.

That being said if you wanted to remove some wood to let the bolt sit further forward I reckon you could get some dowelling about the size of the butt-screw access and fix some sand paper to the end, then just spin it around, clean it out, and repeat until you have the correct protrusion. DON'T TRY THIS until the experts give their input however.