Transcendence

They also seem to be able to spawn in from directions where I've already killed the Iocrym outpost.

Note that the Iocrym waves begin once you complete (or fail) a mission or destroy an Iocrym outpost. Try and attempt to do as many missions as possible first, rather than attacking the outposts. But I agree, Heretic as a whole can be quite tedious and frustrating at times.

It's unclear why the human bases weren't wiped off the map while the player was still back in Eridani.

Perhaps they didn't think Humans had the technology to break the quarantine. Once research ramps up and the threat of Humans escaping the quarantine zone intensifies, the Iocrym decide to take action.