So, it appears that if I have the technical abilities required to open the gate near the NPC I have to save which leads me to a safe way out of the Wraiths' base, the game does not acknowledge that! But, if I turn around and use the same path I go into the room to save the required NPC to progress through this quest, then the game will ask me to "Get in the back of the van". I used a different save data where I didn't step inside the whole area yet to see if that could trigger the bug again, and it happened anyway.
Now I am curious to know if I am the only one who ran into this exact same bug.
Now I am curious to know if I am the only one who ran into this exact same bug.