How do you make defences stronger?

I'd always thought that researching stronger base structure materials would make my defence structures stronger.

I was wrong.

It's actually the research of stronger walls (though to Plasteel Mk3) that makes them stronger.

Base structure materials only applies to factories, HQ, repair/rearm, and things like that. You should still research a few though, because sooner or later enemy VTOLs will target your factories.