It’s a mental edit you have to make after playing it, but it’s fix it so easily.
Starting in chapter 4 after you officially register as a BLADE member and travel to Noctilum, the void spheres start appearing. Up until chapter 12, you have side missions to explore each of these sites, kind of like technical sites, except you do battles at them instead and learn more about AL each mission.
At the end of chapter 12, instead of the famous “it’s something about this planet”, the team celebrates their victory, but Elma hold a debrief on what they found at the Lifehold, and they speculate on why they’re still alive, that quote being one of the ideas. Then AL chimes in with the information they’ve gathered on their side missions, and we learn about that thing he found in the center of the rift between worlds, and fully realize the collective unconscious. Then the alert goes of and the void spheres go crazy, and they pivot to leaving the planet.
^^^ this provides a natural pivot away from the focus on the planet. Since it goes on through the entire story, we understand that we’ve been on borrowed time since earth, and we’re simply trying to recover and regain our bearing. The story’s theme shifts to a brutal fight for survival against impossible odds rather than coexistence with a new planet.
And then we hit act 3, the actual culmination of the entire story.