I actually believe the larger clearance you are referring to, may be for the Bolt head to Washer interface vs Nut to Washer interface. Proper bolts are radiused at the head to shaft junction. Those radius are called out by standards. Since it's not a 90 degree corner, clearance will be needed allow the bolt head to properly seat flat against the washer vs hanging up on the radius.
Given it would double the sizes, if there were washers for the bolt head and different washers for the nut end, my guess is they went with the "larger" size for both.