Instead of the base for the alien ships being just a useless manufacturing part, it should actually maintain function, as it is still technically a whole ship. Just with very low hull points because no crystal. It should work just like a normal ship without special module or special weapons until you grow crystals on it. This would give it use for those who make it but are for some reason unable to grow crystals on it because of the awful grind wall. And the crazy amount of materials needed to make it are worthy of being a ship. Just consider it. You already have the model, just add some extra weapon and module hardpoints to it. Xp
The base ships should be seen as actual ships on the top of the Ellydium ship tree, and be accessible from there.
Base Type A: Fighter
Base Type B: Interceptor
Base Type C: Frigate
Base Type D: Destroyer
Base Type X: Spec Class