Preheat the oven to 350°F. Line a standard 12-cup muffin pan with parchment paper liners or lightly grease the cups with avocado oil. In a large mixing bowl, whisk together the oat flour, almond flour, baking soda, baking powder, pumpkin pie spice, cinnamon, nutmeg, and sea salt. In a separate bowl, whisk together the pumpkin puree, eggs, maple syrup, coconut sugar, avocado oil, and vanilla until smooth.
Pour the wet ingredients into the dry ingredients. Gently stir until everything is just combined. Avoid overmixing the batter.
In a small bowl, beat the softened cream cheese, maple syrup, and vanilla until smooth and creamy.
Divide the pumpkin muffin batter evenly among the 12 prepared muffin cups, filling each approximately 3/4 full.
Spoon approximately 1 tablespoon of the cream cheese mixture into the center of each muffin. Gently press the filling slightly into the batter, leaving some cream cheese visible at the top.
Sprinkle the pumpkin seeds over the muffins. For a slightly sweeter topping, combine the coconut sugar and cinnamon and sprinkle a small amount over each muffin.
Bake for 20 to 24 minutes, or until the pumpkin portion is set and a toothpick inserted into the cake portion comes out clean or with a few moist crumbs.
Allow the muffins to cool in the pan for 10 minutes before transferring them to a wire rack. The cream cheese centers will continue to set as the muffins cool. Enjoy slightly warm, or let them cool completely before storing in the refrigerator.