Prepare the pan. Grease a 9x13-inch baking dish with butter or non-stick cooking spray, or line it with parchment paper for easy removal.
Make the peanut butter mixture. In a medium saucepan, combine the honey and granulated sugar. Heat over medium heat, stirring constantly, until the sugar dissolves and the mixture just begins to boil. Remove from heat immediately to prevent the sugar from overcooking. Cooking it too long will result in hard scotcheroos. Stir in the peanut butter, vanilla extract, and a pinch of sea salt until smooth and fully combined.
Combine with cereal. In a large mixing bowl, pour the warm peanut butter mixture over the crispy rice cereal. Stir gently but thoroughly to coat the cereal evenly.
Assemble the base. Transfer the mixture to the prepared baking dish. Press it down gently and evenly with a spatula or just slightly wet your hands with water to form a compact layer. Set aside.
Melt the topping. In a microwave-safe bowl, combine the butterscotch chips and semi-sweet chocolate chips. Heat in 20–30 second intervals, stirring between each, until fully melted and smooth. Alternatively, melt the chips in a heatproof bowl set over a pot of simmering water (double boiler method).
Spread the topping. Pour the melted chocolate and butterscotch mixture over the cereal layer. Spread evenly with a spatula or the back of a spoon to cover the entire surface.
Cool and set. Allow the Scotcheroos to cool at room temperature or refrigerate them for about 1 hour, or until the topping is set and firm.
Slice and serve. Once fully set, cut into squares or bars. Garnish the scotcheroos with flaky salt, if desired, for an added touch of flavor, and enjoy!