Combine 4 1/2 cups flour, yeast, 2 tablespoons brown sugar, salt, 8 tablespoons butter, and 1 cup of water in the bowl of a stand mixer. Mix with dough hook on low until a dough forms, adding more water if it doesn't come together and flour is loose. Once the dough comes together, knead on medium for about 4 minutes. The dough should be smooth and elastic once ready, and you'll be able to form a windowpane with a piece of the dough. Place in an oiled bowl, cover with plastic wrap, and let rise in a warm place for 1 hour, until doubled.
About 10 minutes before you want to make the pretzels, make the cookie dough. Using the paddle attachment of the stand mixer, cream the 16 tablespoons softened butter with the sugars for about 3 minutes, until fluffy. Add vanilla and eggs and beat until combined. Turn mixer to low and gradually add the flour, mixing until just barely combined. Add chocolate chips.
Once you've made all the pretzels, mix together 2 teaspoons baking soda with enough water in a bowl to submerge a pretzel. Dip each pretzel, then replace on the sheet. Brush with egg wash if desired. Sprinkle with coarse salt or sugar; this is optional, but I think it would have been really good on the bready ends of the pretzels. Bake in a preheated 425F oven for 15 minutes, rotating your pans and switching their positions halfway through baking. Serve warm, but they're also good at room temperature