In a medium bowl, whisk together the flour, baking powder, baking soda, kosher salt, cinnamon, ginger, and nutmeg. Whisk thoroughly so the leavening agents and spices are evenly distributed. Set aside.

In a large mixing bowl, beat the softened butter, granulated sugar, and brown sugar on medium speed for 2–3 minutes. The mixture should look creamy, smooth, and slightly lighter in color. Scrape down the sides of the bowl as needed.

Beat in the egg and vanilla extract until combined. Add the pumpkin puree and mix on low speed just until smooth. The mixture may look slightly separated because pumpkin contains a lot of moisture. This is normal and will come together once the flour is added.

Add the dry ingredients to the pumpkin mixture in two additions. Mix on low speed or fold with a rubber spatula until no dry flour remains. The dough should be thick, soft, and sticky, more like a very thick cake batter than traditional cookie dough.

Cover the bowl and refrigerate the dough for 30 minutes. The chilled dough should be noticeably firmer and easier to scoop. This helps the cookies bake into rounded cakes rather than spreading excessively.

Preheat the oven to 350°F (175°C). Line two large baking sheets with parchment paper. Position one rack in the center of the oven for the most even baking.

Use a 2-tablespoon cookie scoop to divide the dough into 24 portions. Place 12 portions on each baking sheet, leaving about 2 inches between them. If necessary, gently smooth the tops with the back of a lightly dampened spoon so the rounds bake evenly.

Bake one sheet at a time for 10–12 minutes. The cookies should look puffed and matte on top, with set edges and centers that spring back lightly when touched. Do not wait for deep browning; pumpkin cookies remain fairly soft and lightly colored even when fully baked.

Let the cookies rest on the baking sheet for 5 minutes. Transfer them to a wire cooling rack and cool for another 25 minutes. Bake and cool the second sheet the same way. The cookies must be completely cool before filling.

In a clean mixing bowl, beat the softened cream cheese and butter together on medium speed until smooth. Add the sifted powdered sugar, vanilla extract, and fine salt. Beat on low speed until incorporated, then increase to medium speed and mix until thick and creamy. If the filling feels too soft to pipe, refrigerate it for 10–15 minutes.

Pair the cooled pumpkin cookies by similar size: Pipe or spread about 2 tablespoons of cream cheese filling onto the flat side of one cookie from each pair. Top with the matching cookie, flat-side down, and press gently until the filling reaches near the edges.

Arrange the assembled whoopie pies in a single layer and refrigerate for 20 minutes. This firms the filling and helps the sandwiches hold together neatly. Dust lightly with the optional powdered sugar just before serving, if desired.