I would allow my players to craft their own story. I would just present them with a Warrant and Ship I created, then I would let them make the adjustments they want.
I always allow them to craft their own story, whether or not they do so is a different aspect all together. The Warrant and Ship creator assists them in doing so, in a more linear way.
Taking the ship option away from groups, is, IMHO, detracting from the game. They designed it so the players get to choose their own ship, and incorporate what they want into it. Yes yes, I know that when you have a campaign in mind, and they create a Transport ship with asteroid mining rigs instead of a Frigate or Light Cruiser with temples and lances, it can somewhat mess with your story, but that's part of the fun in it for me. The unexpectancy of the game, the thrill of not truly knowing what to expect out of the players and their desires within the game. And the ship is part of that for the players. It's has a past, present, and future story for the players. Just giving them a ship that I create means very little to them, and doesn't do anything to express their ambitions/desires within the game.
For a collection of fan created material, please refer to the link below. Some of it was edited/created by myself and friends, with most is other fan material. Happy gaming people.https://drive.google.com
<p>-"May your endeavors always be prosperous, though they may not always be profitable."