Preheat the oven to 350°F (175°C). Line the baking pan with parchment paper, leaving an overhang on two sides, and lightly grease the paper.
Make the swirl first. Beat the cream cheese and 1/4 cup granulated sugar for about 1 minute, until completely smooth and lump-free.
Beat in the pumpkin puree, egg yolk, pumpkin pie spice, vanilla, and 1 tablespoon flour until smooth. Set aside.
In a large microwave-safe bowl, melt the butter and chopped chocolate together in 30-second bursts, stirring after each, for about 1 1/2 minutes total, until smooth. Let the mixture cool for 5 minutes so it won't scramble the eggs.
Whisk the granulated sugar and brown sugar into the chocolate mixture. Add the eggs one at a time, whisking well after each, then whisk in the vanilla until the batter looks glossy and thick, about 1 minute.
Add the flour, cocoa powder, and salt. Fold with a spatula just until no dry streaks remain; do not overmix.
Spread about two-thirds of the brownie batter into the prepared pan in an even layer.
Spoon the pumpkin mixture over the brownie layer in large dollops, then spoon the remaining brownie batter in dollops between them.
Drag a butter knife through the batter in a zigzag or figure-eight pattern, 3-4 passes in total. Stop while the swirls are still distinct, because over-swirling blends the colors.
Bake for 32-36 minutes, until the brownie edges are set, a toothpick inserted into the chocolate portion comes out with a few moist crumbs, and the pumpkin center has only a slight jiggle.
Cool in the pan on a wire rack for 1 hour, then refrigerate for 30-60 minutes for the cleanest slices.
Lift out using the parchment overhang and cut into 16 squares, wiping the knife clean between cuts.