That and an upgraded engine isn't always going to result in higher resale price. There was an L96 upgrade for about 3K and an LS3 engine upgrade in my boat for about $9K new, the boat already has so much power that it isn't really much of an adder in the resale market except to a select few. Might make the boat sell faster and you might get some more money for it but nothing near the original upgrade cost.
I'm more than willing to pay for the upgraded engine...assuming you can even find the desired boat where someone actually selected it. As a buyer and not a seller, I'm happy to see low option prices on the upgraded engine if you have a seller that thinks NADA is credible. I think a lot of people have your explanation in mind because so few people actually seem to get the upgraded engine. It's five liter city in bowriders from what I see.