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 spice, cinnamon, baking powder, baking soda, and salt and whisk to blend evenly. Add dry ingredients to the pumpkin mixture and fold in slightly. Before fully incorporated, add the milk and fold until combined. Cover the bowl and let rest for 30 minutes.

Meanwhile, in a small bowl, combine softened cream cheese, sugar, flour, and vanilla. Beat until smooth. Add milk and mix until combined. Transfer filling to a piping or zip-top bag.

Use a 2 oz scoop to divide batter evenly among prepared muffin cups, filling to the rim. Snip the tip off of the piping bag and place it in the center of the batter, about ¼ inch deep, to make a swirl. Use all of the filling for the 12 muffins.

Sprinkle chopped pumpkin seeds over the pumpkin batter, pressing in slightly.

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