If this guy working on your boat is asking questions like this perhaps he should not be working on your boat? Especially if he feels NPS & NPT are a safe match because he got "five" threads... Really makes you wonder why we pay so much for these "experts" to work on our five, six and seven figure toys...
Yeah, you're preaching to the choir on that one. The guy's a good guy, and he's a generator guy who's installing our genset, so he's adding a through hull. In fairness to him, this is the way he's always seen it, this is the way he's always done it, he's never had a problem or even heard of a problem. Plus, he's not a fibreglass guy or plumber. It's sort of like asking your plumber why he makes the electrical connections on the water pump in an odd way. It's something he does, but it's not his area of expertise.
In any event, I'm going to invest a number of hours correcting the situation on the through hulls on our boat over the winter, and I'm going to use the flange adaptor, which I learned about from you (thanks so much). I'm actually going to try to do it by keeping the existing through hulls, and add the backing plates and cut the through hulls to length while they're installed. That last part will be the trick to determine whether I can do this without ripping out the actual through hulls, which would make the project substantially more difficult and time consuming.
On another note, I saw on your website one install that I would think twice about. It's the one where you need to make the 90 degree turn right off the through hull, and you attached the elbow right to the flange adaptor, and then the valve after that in the line. To me, that's questionable because you don't have the valve right on the fitting on the hull. So, if the elbow breaks or leaks or whatever, you have no way to shut the water. One disadvantage of the flange adaptor is that you have a fitting between the valve and the through hull (i.e., the flange adaptor itself). To me that's a reasonable compromise under the circumstances. But, adding in the elbow before the valve probably isn't. If it were me (which, as you say on your site, consider how much you're paying for this opinion), I would use a traditional flanged seacock on this one through hull, and fit the elbow to the seacock. That will get you the clearance you need, and still keep the valve right on the through hull.
And FWIW, I wholeheardely concur with others about your website. Very nicely done, and remarkably informative and clear. Thanks.