One idea is when when you're creating a new custom civilization is to make your races ships while in game without actually playing the game. Just use the ship designer while in game. Don't play the game.

Make sure to have cheats enabled to unlock all techs so when get to play screen in ship designer all hulls scales are available to choose from in the in-game ship designer. Save your designs as both ship design and template. Save your game often so you don't lose any designs or saved work.

When you're ready and have all your ships finished make a ship set style for your race from the fleet tab in the Civ Builder. Edit out default ships for your custom ships. When you have completed the set save your race civ. Now no other AI should be able to use your custom ships when playing game.