Mix beef with 2 tablespoons water, 1-1/2 teaspoons salt and baking soda in bowl until thoroughly combined. Use your hands to do this—it's the best way to get it all mixed together. Set aside for 20 minutes.
Adjust oven rack to lower-middle position and heat oven to 275ºF.
Put tortilla chips, cumin, paprika, garlic powder, coriander, oregano, thyme, both chile powders and 2 teaspoons of freshly ground black pepper in a food processor. Process until finely ground, about 2 minutes. Transfer mixture to bowl. Process tomatoes and their juice in food processor until smooth, about 30 seconds.
Heat oil in a Dutch oven or heavy, oven-safe lidded pot over medium-high heat until shimmering. Add onion and cook, stirring occasionally, until softened, 3 to 4 minutes. Add garlic and cook until fragrant, about 45 seconds. Add beef and cook, stirring with wooden spoon to break meat up into small pieces, until beef is browned, 12 to 14 minutes. Add spice mixture and chipotle. Cook, stirring frequently, until fragrant, 1 to 2 minutes.
Add 2 cups water, sugar, tomato puree, tomato paste and beans. Bring to boil, scraping bottom of pot to loosen any browned bits.
Cover the pot, transfer to oven and cook 1-1/2 to 2 hours, stirring occasionally to prevent sticking. (We did 2 hours.)
Remove chili from oven and let stand, uncovered, for 10 minutes. Stir in any fat that has risen to top of chili (it contains flavorful fat-soluble spices), then stir in vinegar and season with salt to taste.
Serve, along with the garnishes you prefer. This chili is even better the next day, so feel free to make ahead of time.