Preheat oven to 400°.
Fill a large pot with water, add one tablespoon of salt, and place on high heat. In a small saucepan, pour in the milk and set heat to medium. Ensure the milk gets hot, but doesn’t boil.
Add the diced pancetta into a French oven (minimum 4 litre capacity). Heat the pan to medium high, and cook the pancetta, stirring every minute or so, until it’s just starting to crisp up, about 7-8 minutes. Add the thinly sliced shallots, and sauté an additional 3-4 minutes, until softened and browned. Transfer to a bowl.
Place the French oven back onto the heat and melt 2 tablespoons of butter. Add the breadcrumbs and thyme and fry until golden brown, stirring often, about 3-4 minutes. Transfer to a small bowl.
Add the macaroni to the boiling water. Cook as per the package instructions.
Meanwhile, begin making a roux by melting a ½ cup butter in the French oven, on medium heat. Add the flour and whisk to combine and continue stirring until the roux begins to become golden, about 2-3 minutes. Pour in the hot milk and whisk until it becomes a creamy sauce free of any lumps. Add all the cheese and stir until melted. Pour in the white wine, stir, then add the cooked pancetta and onions, 1 tablespoon of thyme, chili flakes, salt and pepper. Taste the sauce for seasoning and adjust as necessary.
Add the cooked macaroni directly into the cheese sauce and mix well to get an even creaminess throughout the macaroni. Top with bread crumbs, then place the French oven in the oven. Bake, uncovered, for 20 minutes, until the cheese is bubbling.
Allow to cool for just a few minutes before serving.