Preheat the oven to 350 degrees F.

For the sauce: In a saucepot over medium heat, add the oil, onions, and a pinch of salt. Saute until the onions are tender and translucent. Add the tomato paste at this point and turn the heat up a bit, if needed, to cook the paste. Stir and cook until it deepens in color, and then add the garlic, cumin, and thyme. Stir to blend and cook until fragrant, and then add the crushed tomatoes and beef broth. Raise the heat to bring the mixture to a boil, and then lower to a simmer and cover, simmering for 20 minutes more.

For the beef filling: Meanwhile, in a large pan with straight sides, add the olive oil over medium-high heat. When the oil begins to swirl, add the onions and green and yellow bell peppers. Season with a pinch of salt and saute until the onions and peppers are tender, about 5 minutes. Add the garlic and cook until tender, about 4 minutes more. Add the beef, onion powder, cumin, thyme, Spanish seasoning, tomatoes, and broth, allowing time between each addition to blend. Season with a pinch of salt and a grind or 2 of pepper (the Spanish seasoning adds salt content, so be careful to not over season). Stir and break down the beef into bits using a spoon or fork. Cook until the beef is cooked through, 8 to 10 minutes.

To assemble the casserole: Toss the shredded cheeses together to blend; set aside. Add 1 cup of the red sauce to a baking dish and spread to coat the bottom evenly. Top with 6 tortillas, overlapping to cover the bottom of the casserole dish. Layer the dish by next adding 1/2 of the beef mixture and 1/2 cup of the shredded cheeses, spreading evenly in the casserole. Next, dunk 6 tortillas, one by one, in the warm red sauce and layer over the cheese and beef, overlapping where needed. Top with the remaining beef, another 1/2 cup of the shredded cheeses, and another layer of tortillas dunked in the red sauce. Pour the rest of the sauce over the top, spread evenly, and finish with the remaining shredded cheese. Bake until the cheese is melted and the sauce bubbles, 25 to 30 minutes. Serve hot.