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.

Place the garlic, 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 combine gently without overmixing.

Form the mixture into 32 to 34 meatballs and place them on the baking sheet.

Bake the meatballs until browned and cooked through, about 15 to 20 minutes.

Melt butter in a skillet, then add the onions, thyme, kosher salt, and black pepper. Cook until deep golden-brown, about 25 to 30 minutes.

Sprinkle flour over onions and stir until incorporated. Add wine and scrape up browned bits.

Add beef broth and bring to a boil, cooking until the sauce thickens, about 6 to 8 minutes.

Add vinegar and adjust seasoning as needed.

Transfer meatballs to sauce, coat them, and spread evenly. Sprinkle with remaining Gruyère cheese.

Broil until cheese is melted and bubbly, about 3 to 4 minutes.