Preheat oven to 425?F. Line a standard 12-cup muffin pan with paper liners.

In a large bowl, combine pumpkin puree and both sugars and whisk until smooth and glossy. Add eggs, oil, and vanilla and whisk to combine.

In a medium bowl, combine flour, pumpkin pie spice, cinnamon, baking powder, baking soda, and salt and whisk to blend evenly.

Add dry ingredients to the pumpkin mixture and fold in. Before fully combined, add the milk and fold until the batter is evenly combined. Cover the bowl and let the batter rest for 30 minutes.

Meanwhile, make the cream cheese filling. In a small bowl, combine cream cheese, sugar, flour, and vanilla. Beat until smooth, then add milk and mix until combined. Transfer filling to a piping bag or zip-top bag.

Use a 2 oz scoop to divide batter evenly among prepared muffin cups, filling to the rim. Snip the tip of the piping bag and position it in the center of the batter. Press down to squeeze and create a 1-inch diameter swirl on the surface of the batter.

Sprinkle chopped pumpkin seeds around the cream cheese filling, pressing in slightly.

Bake at 425?F for 5 minutes. Then, reduce the oven temperature to 350?F and bake for another 12-15 minutes until firm when pressed and a toothpick inserted comes out clean. Transfer pan to a wire rack and let cool for 5 minutes before transferring muffins to the rack to finish cooling.