Preheat the oven to 325°F and line an 8x8-inch baking pan with parchment paper, leaving overhang on two sides for easy lifting.
Stir together the gingersnap crumbs, almond flour and melted butter until the mixture looks like wet sand. Press it firmly into the bottom of the pan and bake for 10 minutes, then let it cool while you make the filling.
In a large bowl, beat the cream cheese and brown sugar until completely smooth. Add the yogurt, protein powder, vanilla and salt and beat until creamy, then mix in the eggs one at a time on low speed just until combined.
Scoop 3/4 cup of the plain batter into a small bowl and set it aside. Add the pumpkin puree and pumpkin pie spice to the remaining batter and mix on low until smooth and evenly orange.
Pour the pumpkin batter over the crust and smooth the top. Drop spoonfuls of the plain batter over the surface, then drag a toothpick or skewer through them in loose figure eights to create a marbled swirl.
Bake for 35 to 40 minutes, until the edges are set and the center has a slight wobble. Turn off the oven, crack the door and let the bars cool inside for 30 minutes to prevent cracks, then cool completely on the counter.
Chill for at least 4 hours or overnight until firm. Lift out with the parchment and cut into 16 bars, wiping clean between cuts for neat edges.