Preheat the oven to 425 degrees F. Whisk 2 tablespoons vegetable oil, 2 teaspoons chili powder, the chipotle powder, 1 teaspoon salt and a few grinds of pepper in a bowl. Add the tomatoes and red onion; toss. Roast on a baking sheet, stirring once, until tender, 25 minutes.
Meanwhile, put the squash cut-side up in a microwave-safe dish; add 1/2 cup water, cover with plastic wrap and microwave until tender, 10 to 15 minutes. Let cool; scrape the flesh into a bowl using a fork. Add the roasted vegetables and toss.
Heat the remaining 1 tablespoon vegetable oil and 1/2 teaspoon chili powder in a medium skillet over medium heat. Add the beans and mash with a fork. Bring to a simmer; cook, stirring, until thickened, about 5 minutes. (Add a splash of water if the beans get too thick.)
Heat 1/2 inch vegetable oil in a separate skillet over medium-high heat. Fry each tortilla until crisp, 2 minutes. Spread the beans on the tortillas; top with the vegetables, sour cream and cilantro. Serve with lime wedges.