I would understand if the alterations around a ship were placement of the items on board the ship, As these may not give advantages, And advantages in battles is something that reduces how fair the game is.
Giving people the ability to make their ship better/more powerful than others tends to put others off, It causes one player to end with all the "Cool Gadgets" that make them strong and then other players that just can't quite cut a break and may as well own a row boat in a world of battle ships.
There will become "Best Builds" which takes the fun out of "Here's my ship! And look how I painted the sails" and makes it "Here's my ship, She can destroy a Galleon... While flying at a 90° angle singing God save the queen".
I don't know about you, I love god save the queen, But I'm not wanting to dive into the game after taking a week off due to a family holiday and finding some player has maxed out their stats and become so powerful that no Naval Army can even scratch their ship. I want to sail with my crew in a Galleon and say "Holy mother and Mary! That sloop almost sunk us, And he's solo, That scurvy dog is a legend!"
TL;DR - Needless to say, I want to be able to have a 1 Vs 1 battle with another pirate, And not worry if my bullseye aim is going to beat their potato aim because they have special attributes.