Make the filling first: In a medium bowl, beat the cream cheese and softened butter on medium speed until completely smooth and creamy, 1–2 minutes. Gradually mix in the powdered sugar on low, then add the maple extract and a pinch of salt. Increase to medium-high and whip until light and fluffy, 1 minute. Cover and refrigerate 20–30 minutes to firm slightly.
While the filling chills, preheat the oven to 360°F. Line two baking sheets with parchment paper.
Whisk together the pumpkin puree, eggs, and melted cooled butter in a large bowl until smooth. Stir in the pumpkin pie spice and orange zest. Add the spice cake mix and fold with a spatula just until no dry streaks remain. Let the batter rest 10 minutes to thicken.
Scoop 1-tablespoon portions of batter onto the prepared sheets, spacing about 2 inches apart. For uniform rounds, use a piping bag fitted with a large round tip; smooth any peaks with a damp fingertip.
Bake one sheet at a time for 9–11 minutes, rotating the pan halfway through, until the tops look set and the cakes spring back lightly when touched. Cool on the sheet for 5 minutes, then transfer to a rack to cool completely. Repeat with remaining batter.
Pair the cooled cookies by size. Pipe or spread about 1 tablespoon of the chilled maple filling onto the flat side of half the cookies; cap with the remaining cookies and gently twist to secure. Chill the assembled whoopie pies 15 minutes to set the centers before serving.