Adjust oven rack to middle position and heat oven to 400 degrees.
For the beans: Pulse ingredients in food processor until smooth. Transfer to bowl and cover with plastic wrap.
For the beef: Heat oil in large skillet over medium heat until shimmering. Cook onion until softened, about 4 minutes. Add garlic, chili powder, cumin, oregano, and salt and cook until fragrant, about 1 minute. Add beef and cook, breaking meat into small bits with wooden spoon and scraping pan bottom to prevent scorching, until no longer pink, about 5 minutes. Add tomato paste, sugar, chile, and adobo sauce and cook until paste begins to darken, about 1 minute. Add water, bring to simmer, and cook over medium-low until mixture is nearly dry, 5 to 7 minutes. Stir in lime juice and transfer mixture to plate lined with several layers of paper towels. Use more paper towels to blot up excess grease.
To assemble: Spread half of chips on large serving platter or 13 by 9-inch baking dish. Dollop half of bean mixture over chips, then spread evenly. Scatter half of beef mixture over beans, top with 2 cups cheese and half of jalapeños. Repeat with remaining chips, beans, beef, cheese, and jalapeños. Bake until cheese is melted and just beginning to brown, 12 to 14 minutes. Serve with salsa and other suggested garnishes.