Gunner captains used to be a very occasional thing, mostly for training purposes, since typically only the gunner or pilot can have the necessary situational awareness to co-ordinate with your ally. Pilot should usually mean captain, because gunner captains add a lag between decision and movement, and engineer captains have that plus the engineer having way to much other stuff to think about.
That said they changed it because trolls. Also because some players decided they wanted to fly certain ships, but didn't want to pilot or captain them, often without a clue if the ship was suitable or not because achievements. I would say if you want the responsibility of picking ship configuration then you are also taking on the responsibility of making that ship work which means you are managing it. If you pick the ship you are the de facto captain and I've no problem with the mechanics enforcing that.
As far as doing it for customization reasons, I'm probably not the guy to ask about that. I will say whoever is captain should be in command and feel like the ship is theirs, and having some other players customizations wouldn't appeal to me. I think if you want to be on your ship, then it needs to be yours with you are in command.
I will say this is not going to be a long term problem for you. Outside of training up a new pilot no one uses gunner captains, because pilot captains are just more effective. If you want to stay competitive as you improve in the game either your friend is going to need to get in a place where they can communicate, or you are going to have to take the helm.
It would be nice to have ships restricted to exactly one pilot and at most one gunner, maybe with 'vet' level players allowed to override it by unanimous vote on a ship to let them nerf themselves.
