In a large bowl, whisk together the all purpose flour, rolled oats, baking soda, and kosher salt until evenly combined; set aside.
In another large bowl, beat the room-temperature unsalted butter, packed brown sugar, and granulated sugar with an electric mixer on medium speed until light and fluffy, about 3 minutes.
Add the egg and vanilla extract to the butter-sugar mixture and mix until combined, scraping down the bowl as needed.
Beat in the peanut butter until uniform, then on low speed add the dry ingredients and mix just until combined; do not overmix.
Fold in the broken pretzels, M&M's, and milk chocolate chips until evenly distributed.
Cover the bowl and refrigerate the dough for at least 3 hours or overnight to firm up.
Preheat the oven to 350°F (175°C). Line baking sheets with parchment paper or silpat mats.
Use an ice cream scoop to portion the chilled dough onto the prepared baking sheets, spacing about 2 inches apart.
Bake for 12 to 13 minutes, until the edges are lightly browned.
Remove from the oven and, if desired, sprinkle with flaked sea salt. Let cookies cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely.