Preheat oven to 400°F. Butter 11x7x2-inch glass baking dish. Melt 3 tablespoons butter in heavy large skillet over medium-high heat. Add shallots; sprinkle with salt and pepper. Cover and cook 5 minutes, stirring often. Reduce heat to medium. Cook, covered, until shallots are deep brown, stirring often, about 6 minutes.
Meanwhile, cook macaroni in large saucepan of boiling salted water until just tender but still firm to bite, stirring occasionally; drain well. Reserve pan. Bring half and half and hot sauce to simmer in same saucepan over medium heat. Toss cheddar cheese and flour in medium bowl to coat; add to half and half mixture. Whisk until sauce is smooth and just returns to simmer, about 2 minutes. Stir in bacon. Mix in pasta. Season with salt and pepper.
Spread pasta mixture in prepared dish. Top with shallots, then gorgonzola cheese. Sprinkle with pepper. Bake until heated through, about 15 minutes.