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 ground beef and use fingers to combine without overmixing.

Form the mixture into 32 to 34 meatballs (about 2 tablespoons each). Place on the baking sheet, spacing them about ¾-inch apart.

Bake on the middle rack until browned and cooked through or until an instant-read thermometer inserted into the center of a meatball registers at least 165°F, 15 to 20 minutes. Meanwhile, make the sauce.

Melt the unsalted butter in a skillet over medium heat. Add the onions, 1 tablespoon of the thyme, remaining kosher salt, and remaining black pepper. Cook, stirring frequently until the onions are very soft and golden-brown, about 25 to 30 minutes.

Sprinkle all-purpose flour over the onions and stir until incorporated, about 1 minute. Add dry white wine and scrape up any browned bits. Continue to stir until the wine is evaporated, about 30 seconds.

Add beef broth and whisk to combine. Bring to a boil and cook until the sauce thickens, 6 to 8 minutes. Remove from heat and add vinegar. Taste and season with more salt and pepper if needed.

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

Transfer the skillet to the upper rack and broil until the cheese is melted and bubbly, 3 to 4 minutes. Garnish with remaining thyme leaves and serve with crusty bread if desired.