Preheat your oven to 350°F (175°C) and line a standard 12-cup muffin tin with paper liners. Lightly spray the liners with cooking spray to prevent sticking.
Prepare the cream cheese filling by beating the softened cream cheese with ¼ cup sugar until smooth and fluffy, about 2 minutes. Add the egg yolk and 1 teaspoon vanilla, mixing until just combined. Set aside.
In a medium bowl, whisk together the flour, pumpkin pie spice, baking soda, and salt until well combined.
In a large bowl, combine the pumpkin puree, granulated sugar, and brown sugar, mixing until smooth. Add the eggs one at a time, then pour in the oil and vanilla, mixing thoroughly after each addition.
Gently fold the dry ingredients into the pumpkin mixture using a rubber spatula, stirring just until no flour streaks remain. Be careful not to overmix, which can make the muffins tough.
Fill each muffin cup about ⅔ full with the pumpkin batter. This ensures room for the cream cheese filling and proper rising.
Add a generous tablespoon of cream cheese filling to the center of each muffin. You can use the back of a spoon to slightly press it into the batter.
If using the optional topping, combine the chopped nuts and turbinado sugar in a small bowl, then sprinkle over each muffin.
Bake for 22-25 minutes until a toothpick inserted into the pumpkin part (not the cream cheese) comes out with just a few moist crumbs. The tops should spring back when lightly touched.
Allow the muffins to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely. The cream cheese center will be quite soft when warm but will firm up as they cool.