I think what is missing here is the understanding that in his builds he's talking about a completely new installation. The trans is mounted first, the coupling for the shaft installed with a dummy shaft - and the intermediate and strut glassed into place based on the position of the shaft. unless the trans comes out, this never changes. Replace the engine, no need to realign.
Going from one trans to another....sure, I see that you'd have to align.
I can not think of any reason that he's ever be in a position to need to shim though. When the boats he works on go from 400 to 600 hp engines, he takes the old trans out... as well as the intermediate and strut... and starts all over with the new trans. If he had a particular trans fail, he'd figure out why and reinstall the same rather than switching brands or models to solve a problem.
Get one end fixed in place (such as the rudder), mount the trans and fill in the rest of the pieces. I thing too many jobs get overly complicated and later have issues) because of trying to "make something work" instead of doing it right. Part of doing it right is understanding why something failed, not just upgrading/changing and hoping it will work out.