Place the brisket in a resealable bag or container. Blend the tomatoes, lager, cumin, chile powder, cocoa, oregano, vinegar, chipotle, 1 tablespoon of adobo sauce, sugar, 1 teaspoon of salt, and pepper until smooth. Pour the marinade over the brisket, seal the bag, and refrigerate overnight to allow the flavors to soak in.
Preheat the oven to 300°F. Transfer the marinated brisket to a Dutch oven and add bay leaves. Bring it to a simmer on the stovetop, then cover and place in the oven. Cook for about 3.5 hours, or until the beef is tender and shreds easily with a fork. Remove the meat from the liquid, discard the bay leaves, and shred into bite-sized pieces. Combine with some reserved cooking liquid, and season if needed.
Combine the shredded cheddar, Velveeta, and cornstarch in a bowl. Add the milk and adobo sauce to a medium saucepan, then stir in the cheese mixture. Cook over low heat, whisking frequently, until the sauce is velvety smooth.
Heat oil in a saucepan over medium heat, then sauté the onions for 30 seconds. Add the vinegar, water, oregano, sugar, and a pinch of salt. Stir, remove the pan from heat, and allow the onions to cool to room temperature.
Preheat the oven to 350°F. Spread tortilla chips in a single layer on a baking sheet. Drizzle the warm cheese sauce over the chips, followed by the shredded barbacoa. Sprinkle on mashed pinto beans, pickled jalapeños, olives, and diced tomatoes. Bake for 7-8 minutes, just until warmed through.
Top the nachos with dollops of sour cream, chopped cilantro, and the pickled red onions before serving. Serve warm with salsa on the side.