Beat cream cheese, 2 tablespoons sugar, and 1/2 teaspoon vanilla until smooth. Scoop into 18 small mounds (about 1 teaspoon each) on a parchment-lined plate. Freeze for 30 minutes until firm. This prevents the filling from melting into the cookie during baking.

Beat butter, brown sugar, and 1/4 cup granulated sugar on medium speed until light and fluffy, about 3 minutes. Add pumpkin puree, egg yolk, and 1 teaspoon vanilla; beat until combined. The mixture will look slightly curdled - this is normal.

Whisk together flour, pumpkin pie spice, baking soda, and salt. Add to wet ingredients and mix on low just until no dry streaks remain. Do not overmix. Chill dough for 30 minutes to make it easier to handle.

Preheat oven to 350F. Line baking sheets with parchment. Scoop 2 tablespoons dough, flatten slightly in your palm, place a frozen cheesecake mound in the center, and wrap dough around to seal completely. Roll into a ball, then roll in granulated sugar. Place 2 inches apart on prepared sheets.

Bake 12-14 minutes until tops are set and just starting to crack. The centers should still look slightly underdone - they will firm up as they cool. Let cool on sheets for 10 minutes before transferring to a wire rack. Cool completely before serving.