Preheat oven to 325°. Tie roast with kitchen twine at 1” intervals; season with salt and pepper.

Heat oil in a large ovenproof pot over medium-high heat. Cook onions, stirring occasionally, until soft, 10–15 minutes.

Add wine, vinegar, and sugar. Bring to a boil, reduce heat, and simmer until reduced by half, 10–12 minutes.

Add garlic and broth and return to a simmer; add roast and thyme. Cover and braise in oven, turning roast occasionally, until roast is tender, 2½–3 hours.

Transfer roast to a large baking dish and strain braising liquid over. Cover and chill onions. Cover and chill roast at least 12 hours.

Combine onion and vinegar in a medium bowl. Let sit 30 minutes; drain. Add chile, basil, chives, parsley, and lemon zest and toss; season with salt and pepper.

Scrape fat from beef; discard. Transfer beef to a cutting board. Bring solidified braising liquid to a boil in a large saucepan.

Reduce heat and simmer, stirring occasionally, until reduced to 2 cups, 25–30 minutes. Add vinegar and braised onions; season sauce with salt and pepper.

Place flour in a shallow bowl. Remove twine from roast and slice into eight 1–1½” pieces; season with salt and pepper.

Heat oil in a large nonstick skillet over medium heat. Working in batches, dredge meat in flour and cook until browned and crisp, about 4 minutes per side.

Arrange on a platter and drizzle with sauce; top with gremolata.