The Wizard's tower doesn't protect Agnieszka from the Wood—it protects her from herself.
This is the system's true mechanism, and the book's design choices expose it unflinchingly.
She lives in a room at the top of a structure explicitly coded as ascending toward purity and descending toward rot. The Wood seeps up from below, contamination rises, cleanliness lives overhead—to go down is to risk corruption, and to stay up is to remain dependent on a man who controls the only staircase.
But here's what the narrative structure does to itself: Agnieszka's actual agency emerges the moment she violates the tower's spatial logic. She descends, touches contamination, speaks to Kasia in the Wood—and she doesn't become corrupted, she becomes effective. The tower promised protection in exchange for obedience, but it delivered isolation in exchange for a story about danger. The Wood was never really the threat. Her own will to move through space unsupervised was. The Wizard's tower doesn't fail to contain her—it succeeds so thoroughly that when she finally acts, the text frames her descent as a betrayal that requires redemption.
The system's genius is that it convinced her too. She feels guilty for having been right, feels contaminated for having left—and even after she saves her village, even after she discovers the Wizard's lies, she returns to the tower, not because it protects her, but because she believes she needs protection from what happens when she doesn't stay put.
Draw a floor plan of the tower from memory or the text and notice which scenes happen at each level—then read interviews with Naomi Novik about the book's spatial design choices, which barely exist, which itself is the point.
Find Kate Elliott's essay on how fantasy architecture mirrors domestic control in SFF Signal or Strange Horizons; it doesn't mention Uprooted but it will reframe every room in that tower.