Preheat oven to 375°F (190°C). Spray 6 alternating cups of a 12-cup muffin pan with baking spray with flour.
In a medium bowl, whisk together flour, baking powder, salt, and nutmeg.
In a large bowl, whisk together brown sugar, milk, oil, egg, and vanilla. Gradually add flour mixture, stirring until almost combined. Add pecans, and stir until combined and no dry streaks remain.
Spoon 2½ tablespoons (39 grams) batter into each prepared muffin cup. Spoon 2½ teaspoons (12.5 grams) Cream Cheese Filling into center of batter in each cup. Top each with 2½ tablespoons (39 grams) batter. Fill empty muffin cups about two-thirds full with water. (See Note.)
Bake until browned and domed and a wooden pick inserted in center comes out with a few moist crumbs, 15 to 18 minutes. Let cool in pan on a wire rack for 10 minutes. Remove from pan, and top each with 2 tablespoons (45 grams) Pecan Pie Glaze. Let stand until glaze sets, about 5 minutes. Store in an airtight container for up to 3 days.
