The argument has been made in the Flagship suggestion thread for specific ship traits for pirates only. CJ has reacted positively to that suggestion. The suggestion was not made by a pirate.
Its a menu.. choose what suits your play style : the choice in ships is wide.. even wider with traits. The merchant wants extra cargo.. the pirate extra cannon : each produces a different version of what can be the same ship : valuable to one.. worthless to the other.
The initial discussion on Ship Hand technology is raising the idea of being able to convert ships to add cargo and lose cannon.. or vice versa.
Fact is a pirate can do okay with a very modest ship with not always helpful traits. But a skilled pirate with a ship set-up to maximise their chances, who trades their assets, however gained, to boost their 'firepower'... that's a beast to avoid and a profitable beast too.
And if a merchant or privateer has a similar ship..what matters it to you? Its what you choose to do with your choice of ship that matters.
And if they have a better ship and you want it.. steal it!