I have never seen an engine that the fasteners holding the main caps on are used for alignment, it's just not accurate enough of a way to align the caps.
The machined area on the bottom of the block aligns the caps from left to right, the bolts or studs hold the cap in place fore and aft and help to prevent "cap walk" or the movement of the cap fore and aft as it rocks that can destroy bearings and cranks as well as resist vertical stress. Hence the use of four bolt mains or stronger than stock studs. Personally, if I was a manufacturer, I would use dowels to locate the caps as is used in 14,000-15,000 rpm motorcycle engines producing 170 hp from 1.4 liters of displacement as well as cross bolt the mains through the engine block. I have never seen an engine that aligns a main cap purely by the size of the bolt or stud shank either, but could they have existed in past? Maybe! I was at lunch when I answered the question, so I didn't get into detail.