Melt 4 tbsp butter in a large oven-safe skillet over medium heat. Add onions and a pinch of salt; cook, stirring every few minutes, 40-45 minutes until deep amber and jammy. Meanwhile, cook pasta to al dente; drain and set aside.

Stir sugar into onions; cook 2 minutes. Add broth and sherry (if using), scrape up fond, and simmer until liquid reduces by half, about 5 minutes. Transfer onions to a bowl and wipe skillet clean.

Return skillet to medium heat and melt remaining 2 tbsp butter. Whisk in flour; cook 1 minute. Slowly whisk in warm milk, simmer 3-4 minutes until thickened. Off heat, stir in 4 oz Gruyère and all cheddar until melted. Add thyme, salt, and a generous amount of pepper.

Fold pasta and onions into cheese sauce, stirring until evenly coated. Taste and adjust seasoning.

Preheat broiler with a rack 6 inches from the element. Sprinkle reserved 2 oz Gruyère over pasta. Broil 2-3 minutes until cheese is melted and browned in spots. Serve immediately.