Heat the oven to 350°F. Pan-spray or line two half-sheet pans with parchment paper or silicone baking mats.
In a food processor or blender, grind 50g (1 heaping cup) of the pretzels to a powder and set aside. Rough chop the chocolate with a knife to the size of a dime and smaller (variety is great here) and set aside.
In the bowl of a stand mixer fitted with the paddle attachment, cream together the butter, dark brown sugar, and light brown sugar on medium-high for 4 minutes until well combined. Scrape down the sides of the bowl, add the egg, molasses, and vanilla and mix for 4 more minutes.
Add the flour, ground pretzels, salt, baking powder, and baking soda and paddle on low speed until just combined, about 20 seconds.
Paddle in the remaining 50g (1 cup) of whole pretzels and reserved chopped chocolate until just incorporated.
Using a 2¾-ounce cookie scoop (or a ⅓-cup measure), scoop the dough onto the prepared pans 2 to 3 inches apart. Flatten the domed tops with your palm. Sprinkle flaky salt on top.
Bake at 350°F until brown, 8 to 10 minutes.
Let the cookies cool on sheet pans. Store in an airtight container with a slice of bread for maximum fudginess for up to 3 days.