Perfect Pot Roast With Pickled Onions

Ingredients
Method
Season 3 lb. boneless beef chuck roast, cut into 6 pieces (about 8 oz. each), generously on all sides with some kosher salt, then freshly ground black pepper. Place in an airtight container, cover, and chill 12 hours.
Let meat sit at room temperature 30 minutes before roasting.
Preheat oven to 300°. Place 6 sprigs thyme and 10 black peppercorns on cheesecloth and gather up corners into center; tie closed with kitchen twine. Set sachet aside.
Heat 1 Tbsp. vegetable oil in a large Dutch oven or other heavy pot over medium-high. Working in 2 batches, cook beef until golden brown, about 4 minutes per side. Using tongs, transfer meat to a plate.
Cook 2 medium yellow onions, cut into 2" pieces, 2 medium carrots, peeled, cut into 2" pieces, and 2 celery stalks, cut into 2" pieces, in same pot, stirring occasionally, until beginning to brown, 7–9 minutes. Add one 28-oz. can whole peeled tomatoes, 1 quart low-sodium beef broth, and 1 cup red wine, scraping up browned bits stuck to bottom of pot. Return beef to pot and add reserved sachet. Bring liquid to a simmer; cover pot and transfer to oven. Braise beef and vegetables until fork-tender, about 2½ hours.
Meanwhile, whisk 1 cup apple cider vinegar, 1 tsp. granulated sugar, 1 Tbsp. Diamond Crystal or 1¾ tsp. Morton kosher salt, and ½ cup water in a small bowl until sugar and salt are dissolved. Add 1 medium red onion, thinly sliced (it should be submerged), and let sit at room temperature at least 1 hour.
Using a slotted spoon, transfer meat and carrots to a large plate. Remove and discard sachet.
Transfer remaining liquid and solids in pot to a blender and add remaining 1 Tbsp. Diamond Crystal or 1¾ tsp. Morton kosher salt. Blend until a smooth sauce forms. (Or, use an immersion blender and blend directly in the pot.)
Transfer sauce back to pot, then add beef and carrots. Top with drained pickled onions and some finely chopped chives. Do ahead: Red onion can be pickled 1 day ahead. Cover and chill.