We did not take the black pearl and continuously evolve it directly into the USS Iowa. That is the analogy the article is making. You are objecting to something that isn't in the article.
Look up why submarines have 21" torpedo tubes. That goes back a hundred years. Every other part of the warship has been redesigned and swapped out. The 21" tube has remained. That is a ship of theseus situation.
Your point is that humanity has had a history of green field designs in ship building rather than replacing parts in the same ship. Humanity arrived at coherence by reusing working parts of old designs that turned into defacto standards. This is no different from e.g. a well designed software library working tirelessly for decades.
But how exactly does that prove that the metaphor is bad? It doesn't, it validates it!