Yes, these engines have other uses. But there is an enormous market of yachts, tugs, etc. smaller than what is considered to be a "ship" and bigger than any automotive engine could power. I argued only with the assertion about "automotive engines". It was true when I was a kid that most engines I was around on commercial boats were special versions of automotive engines. It has not been true in my experience for a couple decades.
Depending on the kind of yacht, might also be considerably smaller than an automotive engine. I'm somewhat superficially familiar with sailboat engines, and the market leaders in that segment are Yanmar and Volvo Penta.
Yanmar, AFAIU, is a big maker of various industrial and agricultural engines, so I guess the Yanmar marine engines are variants of those.
For Volvo Penta, I'm quite sure the bigger ones are marinized variants of Volvo car and truck engines, but for the smaller ones, they might sell them also as gensets or such, not sure.
Beyond Yanmar and Volvo Penta, there's a plethora of engine makers (Beta, Nanni, Westerbeke, etc. etc.), which make marinized versions of Kubota engines, which are AFAIU mostly used for agricultural and industrial equipment (e.g. those ubiquitous small Kubota tractors). These are generally well regarded, and sell for considerably less than Yanmar and Volvo Penta.
We love the Kubotas for generators and other small workloads. Nothing else we have would fit in an automobile. The smallest yacht I have worked on had engines with ancestry in locomotives.
As another commenter suggested, I read the assertion about "the largest marine engine manufacturers use mass-produced automotive engines" as "largest engine" not as "largest manufacturer". Maybe the author intended the latter.
"Even the largest marine engine manufacturers use mass-produced automotive engines" means that they use such engines for some purposes, say for the smaller watercraft. It does not mean that they exclusively use automotive designs.
So likely both you and the article author are correct.
