Sunday Roast With Pickled Onions

Name: Sunday Roast With Pickled Onions
Ingredients: 3 lb. boneless beef chuck roast, cut into 6 pieces (about 8 oz. each); 2 Tbsp. Diamond Crystal or 3½ tsp. Morton kosher salt, divided; plus more; 1 Tbsp. freshly ground black pepper; 6 sprigs thyme; 10 black peppercorns; 1 Tbsp. vegetable oil; 2 medium yellow onions, cut into 2 pieces; 2 medium carrots, peeled, cut into 2 pieces; 2 celery stalks, cut into 2 pieces; 1 28-oz. can whole peeled tomatoes; 1 quart low-sodium beef broth; 1 cup red wine; 1 cup apple cider vinegar; 1 tsp. granulated sugar; 1 medium red onion, thinly sliced; Finely chopped chives (for serving); A layer of cheesecloth