Heat the oven to 350°F.
Wrap the flour tortillas together flat in foil and heat in the oven until warm, 10 minutes. While the tortillas are heating, heat 2 Tbs. of the oil in a large, heavy skillet over medium heat and cook the onion, stirring, until golden, about 10 minutes. Add the tomato, chipotles, beans, and 1⁄2 tsp. salt and cook, stirring until heated through, for about 5 minutes.
In a medium nonstick skillet, heat the remaining 2 Tbs. oil over medium heat. Scramble the eggs and crema or milk with a fork and add them to the pan. Cook the eggs, stirring, until curds form, season with the remaining 1⁄4 tsp. salt, and remove from the heat when they’re still slightly moist.
Lay a warm tortilla flat and arrange the fillings in a row side by side: 1⁄4 of the eggs, 1⁄4 of the bean mixture, 1⁄4 of the cheese, 1⁄4 of the sliced avocado, and 1⁄4 of the chopped cilantro. Fold up the bottom of the tortilla over some of the filling and fold in the sides to make an open package. Repeat with the remaining tortillas and serve the burritos immediately.
To make it a Rice and Beans Burrito, substitute 2 cups of warm cooked rice for the eggs.