In a large bowl, whisk together the flour, oats, baking soda and salt. Set aside.
In another large bowl, use an electric mixer on medium-speed to beat the butter and sugars until light and fluffy, about 3 minutes. Add the egg and vanilla extract. Mix to combine. Scrape down the bowl as needed. Beat in the peanut butter. On low speed, add the dry ingredients until just combined. Stir in the pretzels, M&M's and chocolate chips. Cover the bowl, and refrigerate for at least 3 hours (or overnight).
Preheat the oven to 350℉. Line baking sheets with parchment paper or silpat mats.
Using an ice cream scoop, scoop up the dough and place on the baking sheets 2-inches apart. Bake for 12 to 13 minutes, until lightly browned on the edges. Remove from the oven and sprinkle with flaked sea salt (if using). Let the cookies cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely.