Take the shellcore command game for example. Every ship start with a very small body/core that you can build from:
You can then use modules such as hull, wings, weapons, engines to connect and to make the shape of the ship. More modules mean a bigger ship:
I know that the modules in this game and this pack have different scales, but this is just to show that you can create various shapes and ship sizes with just enough modules, no matter the size. In my opinion the secret is the HULL modules. They make the main structure of the ship and connect the body to other modules.
That's what I'm thinking and I hope it's clear!
Also, I really loved the pack, so I'll be doing a game where players can design their own ships from body using other modules. Each module will have it's own property and stats. The engine for example will allow fwd/bwd or strafe movements, depending on the location of the engine. Wings will speed up rotation but also increase the overall mass and so on.