Preheat the oven to 350°F (175°C). Line a 9×9-inch metal baking pan with parchment paper, leaving an overhang on two sides, and lightly coat with nonstick baking spray.
In a large bowl, whisk together the brownie mix, eggs, vegetable oil, and water until smooth, about 1–2 minutes.
Spread the brownie batter evenly into the prepared pan.
Bake for 30–33 minutes, or until a toothpick inserted into the center comes out with a few moist crumbs.
Allow the brownies to cool completely in the pan.
Reduce the oven temperature to 300°F (150°C).
Spread the flour evenly on a parchment-lined baking sheet and bake for 5–7 minutes to heat-treat it, eliminating any harmful bacteria. Allow the flour to cool completely.
In a large mixing bowl, beat the softened butter, brown sugar, granulated sugar, and vanilla extract until light and fluffy, about 1–2 minutes.
Add the heavy cream and salt, mixing until fully incorporated.
Gradually add the cooled, heat-treated flour, mixing just until combined.
Fold in the mini chocolate chips with a spatula until evenly distributed.
Scoop portions of the cookie dough over the cooled brownie layer, then gently spread into an even layer using an offset spatula.
Sprinkle the mini M&M’s evenly over the cookie dough, pressing them in lightly so they adhere.
Refrigerate for 30 minutes to allow the cookie dough to firm up.
Lift the brownies out of the pan using the parchment paper overhang, slice into squares, and serve.