The criteria is not the position of the shaft in the shaft log, but how the flange on the shaft mates with the flange on the engine. The shaft flange will be at right angles to the shaft to a high precision. If it mates with the engine flange then the engine and prop form a straight
line and there will be a minimum of vibration. Remember you are trying to get the gap between the two flanges to vary by less than a couple of thousandths around the circumference. That is a pretty tight tolerance. Also when a boat is moved from stands on the hard to the water, it will take several days for it to completely reform to the new forces.