Adjust an oven rack to the middle position and heat the oven to 400°F. Toss the tortillas with oil and salt on a large baking sheet, then spread them in a single layer. Bake until they are crisp and golden brown, about 12 to 15 minutes.

Heat the remaining oil in a large skillet over medium-high heat until shimmering. Add the chiles, onions, and salt, then cook until the vegetables are softened and starting to brown, about 8 to 10 minutes.

Stir in the garlic and chipotle and cook until fragrant. Add the water and tomatoes, including the juice, and simmer until the sauce has thickened slightly, about 5 minutes.

Carefully transfer the sauce to a blender and process until completely smooth. Return the sauce to the skillet and stir in the beans.

Mash a small portion of the beans directly into the sauce using the back of a spoon or a potato masher—this creates a creamy, cohesive texture. Fold in the baked tortillas until they are well coated.

Transfer the mixture to a 13 by 9-inch baking dish and bake until the sauce is bubbling and the tortillas have softened slightly, about 10 minutes.

Whisk the sour cream and lime juice together in a small bowl. Top the hot chilaquiles with the crumbled cheese, fresh tomato, cilantro, and a drizzle of the lime-cream. Serve immediately, while the tortillas are tender but still have body.