Preheat the oven to 325°F and line a baking sheet with parchment paper.
Beat the cream cheese, powdered allulose, egg yolk, and vanilla bean paste until smooth. Freeze small teaspoon-size portions on a parchment-lined plate for 20 minutes.
Stir almond flour, coconut flour, powdered allulose, baking powder, and salt in a bowl. Mix in the softened butter, egg yolk, vanilla bean paste, and caramel extract until a soft dough forms.
Scoop 12 portions of dough and flatten each one into a thick round. Place a frozen custard portion in the center and wrap the dough around it.
Arrange the cookies on the baking sheet and gently flatten the tops. Bake for 13 to 15 minutes, until the edges are lightly golden and the centers are set.
Cool the cookies completely, then sprinkle each top with granulated allulose.
Broil for 1 to 2 minutes on the top rack, watching closely, until the allulose melts and turns glossy. Let the tops firm up for 5 minutes before serving.