Symbolism, Imagery, Allegory
When Charlie is fourteen, he builds a tree house from scratch. He spends a great deal of time looking for the exact right tree, and finally settles on the Master Oak and draws out detailed floor plans for the space:
I studied the paper. There were two distinct rooms. One had a bed, the other a small futon couch. Up to that point, I'd envisioned a tree house Dietz-style. A piece of old plywood, a rope, and a great imagination. (1.17.20)
The tree house isn't just some kind of clubhouse or kid's play space for Charlie. It's his only means of escape, and the first way that he's able to physically—and emotionally—separate himself from what's going on at home. The tree house is his space, his kingdom where he doesn't have to listen to his parents fight or worry that he's going to end up an abusive jerk like his dad. Building it, then, is an act of laying claim for Charlie, of trying to fathom a different life for himself.
Though the tree house serves as Charlie's safe space, unfortunately it's not far enough away from his family and his troubles to save Charlie. In the end, Charlie invites trouble into his life when he falls in with the wrong crowd and starts inviting Jenny Flick up to the tree house to sleep with him, which Vera calls him out on:
"You let them carve the Master Oak, Charlie." He opened his mouth to say something, but I stopped him. "You took them to the pagoda and played paper airplanes with them. You f***ed them in our tree house, Charlie." (5.5.16)
After that, the tree house isn't a sacred, safe space for Charlie anymore, which is perhaps best exemplified by the fact that he doesn't leave his notes for Vera there (instead he leaves them in the tree). In the end, having a separate place fails to keep Charlie from messing up his life and winding up dead, and because of this, the tree house also symbolizes the impossibility of truly escaping the past. It's a good thing Vera finally decides to look hers in the eye and deal with it, because Charlie's attempts to just hide don't work out.