The crankshafts with the offset holes at the rod journals would be the original design that was changed up in ’56 to the newer ‘side by side’ design as a result of cost cutting and the need to increase production. All things being equal, use the earlier crankshaft with the offset oiling holes at the rod journals. This particular design will have superior oiling characteristics to the cranks that have side by side oil holes on the rod journals.
Also look at the rear of the crank and you’ll likely see where the earlier model ‘offset oil hole’ crankshafts do not have an oil slinger at the rear main while the later model ‘side by side oiling’ crankshaft does incorporates the oil slinger. The early blocks that did not incorporate the oil slinger on the rear of the crankshaft are usually not machined to accept the later model crankshafts with the oil slinger so that’s something to watch out for. Whereas using the early crankshaft fits all years of production Y blocks, the '56 and newer cranks may not fit in the '54 and '55 blocks without machining most of the oil slinger off of the crankshaft.
As an FYI, the offset ground stroker crankshaft that’s in Bob Martin’s ’56 Merc uses the earlier design crankshaft with the offset oiling holes at the rod journals. When given the choice, the earlier cranks with 'offset oiling holes' are an all around better design as opposed to those with 'side by side' oil holes. If you look at the amount of work it takes to put the oil holes away from each other or 'offset' rather than 'side by side', it becomes evident how labor and machine intensive a process it was to accomplish this. Hence the move to just put the oil holes side by side.
Lorena, Texas (South of Waco)