As others have said, no matter how stiff or well built the boat, some movement is realized when going from the trailer to water. That being said, there is also flex while under power, turning, etc that changes the alignment slightly in those situations as well. The only variable is how much flex is experienced and is it too much change to then cause alignment issues when in the water/under power. Since most folks have had zero alignment related problems (bearing/seal failure, excessive vibration, shaft binding, etc) with their MC boats after doing the alignment on the trailer, the amount of deflection seems to not be so severe as to cause issues- likely due to the smaller amount of deflection found in MCs vs other brands due to more robust construction (If it was a Bayliner, they would probably have to use a flex coupling instead of a rigid coupling as they are real flexy fliers
). Bottom line is If you want it the closest to perfect, do the alignment in the water but you will likely never know the difference.