The only way to change a ship's design is to retrofit.
AFAIK, all created Warppoints are stable. MM could probably easily add a new ability for creating unstable ones...
You could design a ship with just engines and armor and repair.
Or you could create a hull size with built-in engines, MC, and repair, then just add armor when you make designs. You wouldn't be able to restrict the thing to armor only, and players could add anything they want.
If it is just you vs AIs, then it would work.
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