Arrange one oven rack 6 to 8 inches from the broiler and a second rack in the middle of the oven. Heat the oven to 400°F. Line a rimmed baking sheet with parchment paper or a silicone baking mat.

Halve and thinly slice the yellow onions. Pick the leaves from the thyme until you have 2 tablespoons. Mince the garlic. Grate the Gruyère cheese on the large holes of a box grater.

Place the garlic, 2 teaspoons of the thyme, ¼ cup of the Gruyère cheese, panko breadcrumbs, milk, egg, Worcestershire sauce, 1 ¼ teaspoons of the kosher salt, and ¼ teaspoon black pepper in a large bowl and stir to combine. Add the ground beef and use your fingers to combine.

Form the mixture into 32 to 34 meatballs, about 1 ½ inches each. Place on the baking sheet, spacing them about ¾-inch apart.

Bake on the middle rack until browned and cooked through, about 15 to 20 minutes.

Melt the butter in a skillet over medium heat. Add the onions, 1 tablespoon of the thyme, remaining kosher salt, and black pepper. Cook until caramelized, about 25 to 30 minutes.

Sprinkle the flour over the onions and stir until incorporated. Add the wine and scrape up browned bits, then stir until evaporated.

Add the beef broth and whisk to combine. Bring to a boil and cook until thickened, about 6 to 8 minutes. Add vinegar and adjust seasoning.

Remove meatballs from the oven, set oven to broil. Transfer meatballs to the sauce, stir to coat, and spread into an even layer. Sprinkle with remaining Gruyère cheese.

Transfer the skillet to the upper rack and broil until cheese is melted and bubbly, about 3 to 4 minutes.

Garnish with remaining thyme leaves and serve with crusty bread, if desired.