Heat oven to 500ºF
In a 10-inch cast-iron skillet set over medium heat, cook bacon until crisp. Remove bacon from pan and crumble it. Set aside.
Remove pan from heat and our out all but 1 teaspoon of bacon grease. Press dough into the skillet, spreading it to the edge. Spray with cooking oil, then spread with a thin layer of apple butter, leaving a 1-inch border. Top with cheeses. Toss brussels sprouts with vinegar; scatter over the cheeses. Top with bacon and season with red pepper flakes.
Cook over medium heat until the bottom of the crust if crisp, about 5 minutes. Transfer to the oven and bake until the edges of the brussels sprouts begin to char and the dough is cooked through, about 10 minutes.
Remove from oven and cut into 6 pieces.