While the pasta is cooking, place a medium pot over medium heat with the butter. Add the chopped pepper tops to the butter and soften, 2-3 minutes. Sprinkle the flour over the peppers and cook 1 minute more. Whisk the chicken stock and milk into the mixture and bring up to a bubble. Stir in the mustard, season the sauce with salt and pepper and simmer until thickened, 2-3 minutes. Remove the pot from the stove and stir in 1 cup of the cheese until melted. Add the pasta to the cheese sauce and stir to combine.
Mound up spoonfuls of the mac ‘n cheese in the peppers. Sprinkle them remaining cheese and breadcrumbs, and bake until the tops are golden brown and peppers are tender, about 15 minutes.