The STR_ALIEN_BASE mission is not flagged as alien base mission (objective: 2) and is missing other attributes too.
To make it spawn bases, it should look like this, right?
Trajectory P6 is the default, so it does still have a landing in mission zone 4.
Some research seems to have been scrambled:
STR_VESSEL_GOVT_CRUISER (Govt Fusion Cruiser) is no longer obtainable.
STR_MISSION_GOVT_PATROL (Govt Business) has been removed from the research section, though the mission and Bootypedia entries still exist.