Melt butter and olive oil in a large heavy Dutch oven over medium heat. Add the sliced onions and toss to coat in the melted fat. Cover and cook undisturbed for 10 minutes until wilted and translucent.

Uncover, sprinkle with sugar and salt, and reduce heat to medium-low. Cook for 40–50 minutes, stirring every few minutes. The onions will gradually collapse, release their natural juices, and deepen into a rich, mahogany-brown jam with a caramelized fond sticking to the bottom. Add garlic during the final 2 minutes.

Pour in the apple cider vinegar and Worcestershire sauce. Use a wooden spatula to scrape up every bit of browned fond caramelized on the bottom of the pot. Cook for 2 minutes until the liquid reduces.

Pour in the rich beef bone broth. Add the fresh thyme bundle, bay leaves, and black pepper. Bring to a boil, then reduce heat to low, partially cover, and simmer for 25 minutes so the onion sweetness infuses deeply into the broth. Discard thyme sprigs and bay leaves. Season to taste.

While the soup simmers, preheat oven to 400°F (200°C). Arrange baguette slices on a baking sheet and toast for 8–10 minutes until dry and golden (bone-dry bread prevents it from dissolving into mush in the broth).

Ladle hot onion soup into oven-safe ceramic crocks or bowls placed on a rimmed baking sheet. Float 1–2 toasted baguette slices on top of each bowl.

Generously pile the grated Gruyère and Swiss cheese over the bread, allowing some cheese to spill over the rim of each crock. Switch oven to BROIL on high. Broil 3–4 minutes until the cheese is bubbling, blistered with golden-brown spots, and deeply melted. Garnish with fresh thyme and serve steaming hot.