With a good shaft packing so that the shaft is centered in the stern tube, the flange on the shaft is the reference - You don't mess with that. You carefully move the engine so that the transmission flange ends up exactly parallel with the shaft flange and correct up, down, left and right and you use a very fine feeler gauge between the flanges to insure they are exactly parallel - You want an even drag on the feeler gauge as you move it 360 degrees around the flanges
The 'talent' required is to understand which engine mounts need to be adjusted and in what direction to improve the misalignment you have at the moment. Once you have the engine sitting with about equal weight on all 4 mounts, you move them in pairs, front or rear - If you raise the right front half a turn, do the same with the left front. If the two flanges touch at the top and nowhere else, you have to lower the front engine mounts, which will also raise the trans flange a bit because the engine will be pivoting on the rear mounts which are in front of the flange, so the rear mounts will have to be lowered a bit too - Maybe half as much as your front adjustment, but whatever is needed to get the flanges back to the same height
The good news is, even a rank amateur can do this and do a good job of it if you have enough patience. Make small adjustments and keep checking the match of the flanges. Slide the shaft back away from the trans flange a quarter inch or so, make your adjustment and slide the shaft flange forward to check it's match with the trans flange. Figure out what your next adjustment should be, slide the shaft back a quarter of an inch, make the adjustment and slide the shaft forward again and check your work. Repeat 20 or 30 times and you're all set!

You will learn (eventually) what adjustments will improve the match and which make it worse, just keep remembering that the shaft and it's flange is the gold standard and cannot be moved up or down, left or right - Only the engine/trans is moved and the shaft flange is to check your work
You NEVER want to have to pull the two flanges together with the coupling bolts - If they don't freely slide together where a very fine feeler gauge tells you they are touching all the way around, continue the process of moving the engine until you're sure they are absolutely parallel. All the bolts and nuts run down finger tight should give you the same feel with the feeler gauge when you stick it between each pair of bolts - That means everything is parallel
After you've done this on half a dozen boats it doesn't take all that long . . . . maybe an hour or so. Your first attempt may be interrupted by darkness and you'll need to continue the next day, but don't give up on it. Keep working until you get it perfect. A lightbulb will go off when you finally figure out what needs to be adjusted to improve the match and things will speed up after that
There ARE some things you can do a better job of than the guy in the boatyard and this is one of them . . . . and when you do it, you know it's perfect - True, he may get what he considers an 'acceptable' match in only 20 minutes or so, but you can almost guarantee his match will not be as perfect as yours . . . . assuming you take enough time to get it right. If he does it without using a feeler gauge, you don't want him doing it at all, IMO
Don