If I'm not mistaken, modules (and hull types) are unlocked by helping the faction that uses them, like Spire stuff from winning Spire involved scenarios.
It's an achievement. You need to run a 120 planet map to get the 15 nebula and run the cmd line to get duplicates enabled. Out of the 6 repeats, hope you get the rest of the mods. And as far as I remember, reloading saves doesn't change the scenarios.