Preheat oven to 400°F. Coat a 13x18-in. rimmed baking sheet with nonstick spray. Line bottom of pan with parchment paper.
Whisk together flours with baking powder, 2 tsp. cinnamon, and salt in a medium bowl.
Mix eggs, 4 Tbs. melted butter, 1/4 cup maple syrup, vanilla, and milk in a large bowl. Grate 2 apples on the large holes of a box grater (about 2 cups of grated apple). Stir grated apple into wet ingredients.
Stir flour mixture into wet ingredients just to combine. Pour batter into prepared baking sheet and spread into an even layer.
Thinly slice remaining 2 apples and arrange on top of batter. Lightly brush apple slices with remaining 1 Tbs. melted butter. Mix sugar with remaining 1/4 tsp. cinnamon in a small bowl. Sprinkle mixture evenly over apples.
Bake until pancake is golden brown around the edges and a toothpick inserted into the center of the pancake comes out clean, 18 to 20 minutes. Let cool 10 minutes. Slice into 12 squares and drizzle with maple syrup.