Make the sauce: Preheat the oven to 400 degrees F. Toss the tomatillos, onion, jalapeno and olive oil on a baking sheet and season with salt and black pepper. Roast until browned, about 45 minutes. Puree in a blender with the cilantro, thinning with water as needed. Season with salt.
Meanwhile, prepare the omelet: Cook the chorizo in a large nonstick skillet over medium-high heat until crisp, breaking it up, 4 to 5 minutes. Transfer to a paper-towel-lined plate. Stir the cumin, cayenne and paprika into the drippings in the skillet. Add the beans and saute until soft, about 5 minutes. Season with salt and black pepper, then add the bell pepper and cook 1 to 2 more minutes. Transfer to a bowl.
Whisk the eggs and milk in another bowl. Wipe out the skillet, reduce the heat to medium and add 1/2 tablespoon butter. Pour half of the egg mixture into the skillet and cook until the center is no longer liquid, loosening the edges with a rubber spatula and tilting the skillet to let the uncooked egg run underneath. Shake the pan to loosen the omelet, then spoon half of the bean mixture, chorizo and cheese down the center. Fold in both sides to cover the filling, then flip the omelet so it is seam-side down and cook 1 more minute. Repeat with the remaining butter, egg mixture and fillings to make another omelet. Top with the tomatillo sauce and garnish with the crema and tomato.