It's been my understanding that the Spawn Ship for Garden Conquest is (sort of) hard-coded into the MOD itself, rather than as a separate MOD as is often done on servers with custom spawn ships.
It appears that now whatever Keen has changed, has made it so that the Garden Conquest Spawn ship is not being used as the default spawn ship when playing in survival. Instead, we have the new atmospheric lander. Even if you're playing without planets.
This is going to be...Problematic.