Season chicken with salt and pepper. Heat 2 tablespoons olive oil in a large pot over medium–high heat. Working in batches and starting with the largest pieces, add chicken skin side down and cook until deeply golden brown on one side, 8–10 minutes. Flip chicken and continue to cook until browned on both sides, another 3–4 minutes.

Transfer chicken to a large plate or rimmed baking sheet and repeat with remaining chicken, turning heat down ever so slightly during the second batch if needed.

Add 4 cloves of crushed garlic and crushed red pepper flakes to the pot, letting it all sizzle in the chicken fat a minute or two. Scatter over about ¾ of the sliced onions and stir, scraping up any fond from the bottom of the pot. Cook onions about 2–3 minutes.

Return chicken back to the pot, skin-side up, nestling everything in there nice and tight. Add ½ cup vinegar and ⅓ cup water. Season everything with salt and pepper, and drizzle with a bit more olive oil.

Bring to a simmer and reduce heat to medium–low and let cook on the stovetop, uncovered, until chicken is cooked through and sauce is slightly thickened, 8–10 minutes.

Meanwhile, scatter tomatoes and remaining sliced onion on a large serving platter and season with salt. Transfer chicken on top of the tomatoes. Taste the sauce and adjust seasoning if needed. Spoon all the sauce and cooked onions over the chicken and tomatoes and finish with a drizzle of olive oil, flaky salt, more crushed red pepper flakes and black pepper.