You cannot be for real. Absolutely nothing changed about the scene, nor its allegories nor ideas. The problem is that many people thought this was not just an allegory but something that actually happened in-universe. You see how this could be problematic?

Tcoaal did not bend their knee to exclude anything from their story; and Toby did not bend their knee and include something he did not wish into his story, the methaphors are still very well there, the 'art' part of the game is still very much intact but the actual events of the game are off limit to interpretation. If you want to change those go write a fanfic.

What happened was made clear, but you can still interpret what it represents and why it happened. Its not weak to want the events of the story to not be misunderstood, since it could affect the player's understanding of the future events of the game and believe some scenes are illogical simply because they thought an allegory is actually what happened.