Preheat the oven to 350°F. Line 18 muffin cups with paper liners.
For the filling, beat the softened 8 oz (226 g) cream cheese until smooth. Mix in 1 (18 g) egg yolk, ¼ cup (50 g) brown sugar, and 1 teaspoon (5 g) vanilla extract until combined, then set aside.
In a large bowl, mix together 2½ cups (350 g) gluten-free flour blend, ¾ cup (150 g) granulated sugar, ¾ cup (150 g) brown sugar, 2 teaspoons baking powder, ½ teaspoon salt, 1 tablespoon ground cinnamon, 1 teaspoon ground ginger, ½ teaspoon ground nutmeg, and ¼ teaspoon ground cloves.
Make a well in the center of the dry ingredients. Add 2 (100 g) large eggs, 15 oz (425 g) canned pumpkin puree, ½ cup (109 g) vegetable oil, and 2 teaspoons (10 g) vanilla extract, and mix until smooth.
Fill each liner about halfway with batter.
Divide the cream cheese filling evenly among the 18 muffins, about 1 tablespoon each, keeping it in the center and away from the sides of the liners.
Cover the filling with the remaining batter, filling each liner almost to the top.
Bake at 350°F for 20–25 minutes. Insert an instant-read thermometer into the muffin portion, avoiding the cream cheese filling, and look for 200–205°F. Alternatively, insert a toothpick into the muffin portion; it should come out without wet batter. The cream cheese filling will remain soft.
Let the muffins cool in the pan for 5 minutes, then transfer them to a wire rack to finish cooling.