Preheat oven to 350 degrees (F). Line two large cookie sheets with parchment; set aside.
Sift together flour, baking powder, and salt; Set aside.
In a small saucepan over medium-low heat melt 1 stick of the butter, whisking constantly, until it reaches a golden brown color; remove from heat at once. Add the second stick of butter into the brown butter and stir until complete melted.
Transfer melted butter to a large mixing bowl or stand mixer. Add sugars and vanilla; beat until light and fluffy, about 3 minutes.
Add eggs and mix for 30 seconds; the eggs will not be totally incorporated.
Add the dry ingredients in thirds, mixing just until combined.
Stir in the chopped pretzels and toffee bits.
Using a large ice cream scoop or a 2 tablespoon measuring spoon form cookies with the dough and place them on the prepared baking sheet. Press a peanut butter cup in the center of each cookie, then top each with another scoop of dough. Press the dough together lightly around the edges, then press a pretzel in the top of each cookie (optional). Sprinkle with sea salt, then place in the oven to bake for 15-16 minutes, rotating the pan for even color and baking.
Allow the cookies to cool on the baking sheet for at least 5 minutes before transferring to a wire rack to cool completely.
Serve with milk!
Cookies stay good for up to 3 days stored in an airtight container... but I doubt they'll last that long ;)