This is a tough question. First, it is asking about two very different things. A setting will be where something is taking place, and a scene is likely a particular plot event. Second, the question is made difficult because the book has a lot of pivotal moments that occur in a lot of different places. Third, this question is ultimately an opinion question. The answer that I provide might not be the answer that every reader will provide.
I think that I can tie together a location and a scene that I believe are pivotal to the story. The setting location is the Graveyard. The Graveyard is where all of the AWOL Unwinds are hiding until they are 18. At that point, they can't legally be unwound anymore. I choose this location as the most important location because it is where Connor finally begins to see himself as the leader that other people see him as. At the Graveyard, Connor becomes the go to guy when something breaks and needs fixing. Other Unwinds naturally gravitate toward his strong presence, reliability, and relatability. At first, Connor isn't excited about this development; however, he eventually embraces it with a single action. For me, one of the most important parts of the novel is when he traps Roland in the crate. It's this moment that Connor fully commits to standing up to Roland. Through this single act, Connor chooses to become the leader that all of the other Unwinds see in him.