First, preheat the oven to 350ºF and line a muffin tin with muffin liners. Generously spray with nonstick cooking spray.
Prepare the graham cracker crust. Place graham crackers and butter into a high-speed food processor. Process on high until the mixture forms a crumble.
Spoon 1 tablespoon of the graham cracker crumbs into each muffin cup. Use a spoon to press the crumble down into the liners.
Bake the graham cracker crust for 5 minutes at 350ºF. Remove the crust from the oven and allow the crust to cool.
Prepare the chocolate layer. Add the chocolate and coconut oil to a microwave-safe bowl, and microwave on high in 20-second increments, stirring in between until the chocolate is fully melted.
Scoop two heaping teaspoons of the melted chocolate onto the top of the graham cracker crust. Spread it evenly over the crust and transfer the pan to the freezer for 10 minutes.
Prepare the peanut butter layer. Add the cottage cheese, peanut butter, and honey into a high-powered food processor and process on high until thick, creamy, and no lumps. This will take between 2-4 minutes depending on the food processor used.
Scoop 1.5-2 heaping tablespoons of the cottage cheese mixture to the top of the chocolate layer and evenly spread the layer out. Top with mini chocolate chips and flakey salt.
Transfer the pan to the freezer and freeze for at least 2 hours to firm up.