In a large skillet over medium-high; add butter, chipotle pepper, salt, and pepper. Stir to combine. Add 3 cups of milk, then cover.
Once the milk starts bubbling add macaroni. Allow to bubble for 4-5 minutes, until pasta is almost cooked through, stirring occasionally.
Add broccoli and stir to combine. Bubble for 2 minutes.
Meanwhile, in a resealable jar create slurry; combine 2 tablespoons milk and 2 tablespoons flour. Shake until well combined. Set aside.
Preheat oven to broil. Stir in 8 ounces cheese. Add slurry. Stir to combine. Sprinkle with the remaining 4 ounces of cheese. Place under broiler for 2-4 minutes until cheese is melted and golden browned.