Yeah, it's hardcoded. There's a notion of triggers which will likely become mod-accessible eventually, but right now they're too half-baked for that.
Taking a step back, I can certainly see a much more involved mission system for Starfarer, with groups of missions being organized into "tours of duty", with ship/item/character persistence across those, etc. However, that's tangential to the direction of the game overall - it seems more important to forge ahead with the real campaign, rather than to keep adding features to missions. Those kinds of things would be nice to have later, but for now missions are a representation of the kind of battles that would take place in the campaign, and not the more elaborate scripted affairs.
