When using Nexerelin, the abilities from Scan Those Gates are NOT available if and only if a new game is started with the "Tutorial Start" option. That is, solving a minor crisis in the Galatia system.
The abilities from Scan Those Gates show up as normal when using any other starting option.
I speculate that this is because the tutorial start restricts what skills the player has access to and that the abilities from Scan Those Gates get caught in that sweep.