Pat 1 (3-pound) boneless beef chuck roast dry with paper towels. Season all over with 2 teaspoons of the kosher salt and ½ teaspoon of the black pepper.

Heat 1 tablespoon of the olive oil in a large Dutch oven over medium-high heat until shimmering. Add the roast and sear until dark golden-brown on two sides, about 4 to 5 minutes per side. Transfer to a large plate.

Reduce the heat to medium. Add the remaining 2 tablespoons olive oil, 6 thinly sliced large yellow onions, the remaining 1 teaspoon kosher salt, and remaining ½ teaspoon black pepper to the pot. Stir well to combine. Cover and cook undisturbed for 5 minutes. Uncover, stir, cover again, and cook for 5 minutes more.

Uncover and continue to cook, stirring occasionally at first and then more frequently once the onions start to brown, until the onions are a rich caramel brown color, 30 to 40 minutes. Reduce the heat as needed if the bottom of the pot is getting too dark. Make sure to scrape the bottom of the pot when stirring. Meanwhile, arrange a rack in the lower third of the oven and heat the oven to 325°F.

Stir 4 minced garlic cloves into the onions and cook for 1 minute. Sprinkle 3 tablespoons all-purpose flour over the onions, stir well, and cook for 1 minute. Stir in 1 cup dry red wine and scrape up the browned bits from the bottom of the pot. Stir in 2 ½ cups low-sodium beef broth, 5 fresh thyme sprigs, and 2 dried bay leaves.

Return the roast and any accumulated juices to the pot and bring to a simmer. Cover and transfer to the oven. Cook until the meat is gently falling apart when pricked with a fork, 3 to 3 ½ hours.

Skim off some of the fat from the surface if desired. Remove and discard the thyme stems. Shred the roast into bite-size pieces right in the pot with tongs before serving. Garnish with more fresh thyme leaves if desired.