Start by browning the butter. You'll take ¾ cup of butter and melt in a medium saucepan, and then continue to cook past the point of boiling. You will do this over medium heat, past the point of the butter foaming, until it turns a nice golden brown, and has a nutty smell. Make sure you are stirring and watching it, because it will turn from perfectly brown to burnt fairly quickly. Once finished browning, pour into a bowl and allow to cool.
Place browned butter and sugars in the bowl of a stand mixer, fitted with a paddle attachment. Beat on medium-high speed until combined, 2-3 minutes.
Add egg and yolk one at a time, mix until smooth on low speed, about 30 seconds each egg. Beat in the vanilla.
In a separate bowl, whisk together flour, baking soda, salt. Add flour mixture to bowl and mix on low, being careful not to overmix. I usually like to stop mixing when I still have flour remnants around the bowl. Fold in butterscotch and chocolate chips, and pretzels saving a handful to stick on top of the dough balls.
Scoop the dough into large balls. I like to use a ¼ cup cookie scoop. At this point I usually like to chill my dough for a few hours.
Preheat oven to 350 F. Line two baking sheets with parchment paper.
Place 6-8 cookie balls on your baking sheet. Sprinkle with flaked salt. Bake the cookies for 11-12 minutes. You're looking for a nice golden brown outside rim.
Allow cookies to cool on the pan before moving to a cooling rack to hold their shape.