For the Southwestern cornbread strata: Preheat the oven to 350 degrees F. Butter a 10-by-12-inch baking dish and place on a baking sheet. Set aside.
Whisk together the eggs, milk, cream and salt and pepper in a large bowl. Add the cornbread, press to submerge, and let stand, stirring once or twice to soak the cornbread evenly and thoroughly.
Heat the oil in a large cast-iron skillet over medium-high heat, add the sausage, and cook, stirring occasionally, until golden brown. Drain on a paper towel-lined plate. Add the onion, bell pepper and poblano to the drippings in the skillet, season with salt and pepper, and cook, stirring occasionally, until browned in spots and soft, about 5 minutes.
Stir the sausage and onion mixture into the cornbread mixture. Stir in the chopped cilantro, 3/4 cup of the Cheddar and 3/4 cup of the Monterey Jack. Season with salt and pepper. Transfer the mixture to the prepared dish, dot with the goat cheese and sprinkle on the cotija and remaining 1/4 cups Cheddar and Monterey Jack. Bake until the edges are puffed and lightly golden brown and the center still jiggles slightly, about 40 minutes.
For the tomato sauce: While the strata bakes, heat the oil in a medium saucepan over medium heat. Add the onion and cook, stirring occasionally, until soft, about 5 minutes. Add the garlic and cook for 1 minute.
Stir in the tomatoes and chipotle and cook, stirring occasionally, until the sauce is reduced by half and thickened, about 15 minutes. Transfer to a blender and puree until creamy, venting the top of the blender to allow steam to escape. Return the sauce to the saucepan over low heat, and whisk in the crema and salt and pepper to taste; let the sauce heat through and then remove from the heat. Stir in the lime juice and cover to keep warm.
Let the strata rest for about 10 minutes, then serve with the creamy spicy tomato sauce, garnishing each serving with some of the whole cilantro leaves.
When blending hot liquid, first let it cool for five minutes or so, then transfer it to a blender, filling only halfway. Put the lid on, leaving one corner open. Cover the lid with a kitchen towel to catch splatters, and pulse until smooth.