Prepare the Rub and Brisket: In a medium bowl, stir together the dark brown sugar, chipotle chiles, cumin, paprika, salt, and pepper. Rub the sugar mixture all over brisket. Cover with plastic wrap and let sit at room temperature for 1 hour or refrigerate for up to 24 hours.
Prepare the Sauce: Heat the oil in large skillet over medium-high heat until shimmering. Cook the onion until softened, about 5 minutes. Add the tomato paste and cook until beginning to brown, about 1 minute. Stir in the chili powder, chipotle chiles, and garlic and cook until fragrant, about 30 seconds.
Pile the onion mixture in the middle of a 6-quart slow cooker and top with an inverted loaf pan (you can use a metal loaf pan or stack two disposable aluminum loaf pans). Pour the water around the loaf pan. Place the brisket, fat-side-up, on top of the loaf pan. Cover, and cook until a fork inserted into the brisket can be removed with no resistance, 7 to 8 hours on high or 10 to 12 hours on low.
Transfer the brisket to a 9x13-inch baking dish, cover with foil, and let rest for 30 minutes. Remove the loaf pan from slow cooker and pour the onion mixture and accumulated juices into a large bowl and skim the fat. You should have about 2 cups defatted juices; if you have less, add water to make 2 cups.)
Transfer the brisket to a cutting board, slice thinly across grain, and return to the baking dish. Pour 1 cup of reserved defatted juices over the sliced brisket. Whisk the ketchup, vinegar, and liquid smoke into the remaining juices, and season with salt and pepper to taste. Serve, passing the sauce at the table.