Preheat the oven to 400°F (200°C).
On a large baking sheet, toss the chopped red bell pepper, zucchini, yellow squash, and onion with the olive oil; season with kosher salt and black pepper.
Roast the vegetables for about 20 minutes, stirring once or twice, until tender. Remove from oven and let cool to room temperature, then reduce oven temperature to 350°F (175°C).
Grease an 8×8-inch baking pan. In a mixing bowl, combine the roasted vegetables, black beans, mild green chiles, ground cumin, chili powder, paprika, minced garlic, minced jalapeño, and chopped cilantro; season with salt and pepper to taste.
Spread 1/4 cup of enchilada sauce on the bottom of the prepared pan. Arrange a layer of corn tortillas to fully cover the bottom, trimming or tearing tortillas to fit as needed.
Spoon one-third of the vegetable and bean mixture over the tortillas, sprinkle with one-third of the shredded cheese, and drizzle with one-third of the remaining enchilada sauce.
Repeat to make a second layer of tortillas, sauce, filling, and cheese, then make a final third layer of tortillas, sauce, filling, and cheese.
Spray a sheet of aluminum foil with cooking spray and cover the pan tightly with the foil.
Bake covered for 20 minutes. Remove the foil and bake uncovered for an additional 10 minutes, until the cheese is melted and the casserole is bubbling.
Remove from the oven and let rest for 10 minutes before cutting into squares and serving with optional toppings.