Beat the softened cream cheese, powdered sugar, and 1/2 teaspoon vanilla in a medium bowl until smooth. Scoop 18 teaspoon-sized portions onto a parchment-lined plate or baking sheet. Freeze for 1 hour, or until firm.
While the filling freezes, whisk the flour, baking powder, baking soda, salt, and 2 teaspoons pumpkin pie spice together in a separate bowl.
In a large mixing bowl, beat the softened butter, brown sugar, and 1/2 cup granulated sugar until light and fluffy. Add the egg yolk, 1 teaspoon vanilla, and pumpkin puree, then mix until smooth.
Add the dry ingredients to the wet ingredients and mix just until a soft dough forms. If the dough is too soft to shape, cover and refrigerate it for 20 to 30 minutes.
Preheat the oven to 350°F. Line two baking sheets with parchment paper. In a small bowl, stir together the remaining 1/4 cup granulated sugar and 1 teaspoon pumpkin pie spice for the coating.
Scoop about 2 tablespoons of dough and flatten it into a disc. Place one frozen filling portion in the center, then wrap the dough around it and pinch the edges closed. Gently roll into a smooth ball. Repeat with the remaining dough and filling.
Roll each dough ball lightly in the pumpkin spice sugar. Place the cookies about 2 inches apart on the prepared baking sheets.
Bake for 11 to 13 minutes, until the edges are set and the tops are puffed. The centers should still look slightly soft.
Let the cookies cool on the baking sheets for 10 minutes, then transfer them to a wire rack. Store cooled cookies in an airtight container in the refrigerator for up to 5 days.