Got a picture of that? My machine shop already assembled the short block with studs on the main caps. I have an oil pump in a box somewhere in the garage. I guess I could dig it out and maybe see what you're talking about.
Better grab the pump and go visit the machinist..... The stud & nut interfere with the oil pump. Thats why you have to relieve the bearing cap and shorten the stud so you can install a UNMOLESTED nut on the shortened stud.
Drop the pump on the assembled cap and you'll see.... Unfortunately I don't have any pictures. If I remember I'll snap a pic or two when I go to the garage this week.