Prep the pan and oven. Preheat oven to 350°F (175°C).
Line an 8x8-inch pan with parchment, leaving overhang for easy lifting.
Mix the crust. In a bowl, whisk almond flour, coconut flour, sweetener, baking powder, and salt. Stir in melted butter, egg, and vanilla until a soft dough forms.
Par-bake the crust. Press dough evenly into the pan. Prick a few times with a fork.
Bake 10–12 minutes until set and lightly golden at the edges. Let cool 5 minutes.
Blend the pumpkin layer. Beat cream cheese until smooth. Add pumpkin, sweetener, egg, vanilla, spices, and salt.
Mix until silky with no lumps.
Layer and bake. Pour pumpkin mixture over the warm crust and smooth the top. Bake 20–24 minutes, until the center is just set and no longer jiggly.
Cool completely. Place the pan on a rack and cool to room temperature. Then chill 45–60 minutes to make slicing cleaner.
Make the caramel. In a small saucepan over medium heat, melt butter with sweetener.
Cook, stirring, until it deepens to amber, 3–5 minutes (allulose browns; erythritol less so). Carefully whisk in cream, then simmer 3–5 minutes until slightly thickened. Stir in vanilla and salt.
It will thicken more as it cools.
Finish the bars. Drizzle or spread warm caramel over chilled pumpkin layer. Sprinkle pecans and a pinch of flaky salt if using. Chill 15–20 minutes to set.
Slice and serve. Lift out by the parchment.
Use a sharp knife, wiping between cuts, to get clean squares. Serve slightly chilled or at cool room temp.