I just put a rebuilt oil pump in an Oliver 2655 over the weekend and it is the same as you describe. it does not bottom out on crankcase. It has a shoulder further up the pump shaft that seats instead. This had me confused also. You will , however have to look in your repair manual.... there should be a torque value for those bolts ( mine has 2) it is only about 25 ft.lbs.    ...can't remember off the top of my head.
                 Cal