Preheat oven to 400°F.
Stir together oil, chile powder, paprika, cumin, and salt in a large bowl. Add squash, bell pepper, poblano, and onion; toss to coat.
Transfer to a large baking sheet lined with parchment paper; spread in a single layer. Bake until vegetables are tender, 25 to 30 minutes. Transfer to a large bowl and stir in beans.
Cut 12 tortillas in half. Pour ½ cup enchilada sauce over bottom of an 8-inch square baking dish. Arrange 8 tortilla halves over sauce, overlapping as needed, with flat edges of tortillas against sides of dish. Place 1 whole tortilla in center to cover.
Spoon half of vegetable mixture over tortillas. Sprinkle with ½ cup cheese.
Arrange 8 more tortilla halves and 1 more whole tortilla in same manner. Cover with ¾ cup enchilada sauce. Top with remaining vegetable mixture and sprinkle with ½ cup cheese.
Repeat with remaining 8 tortilla halves and 1 whole tortilla. Cover with remaining ¾ cup enchilada sauce and sprinkle with remaining ½ cup cheese.
Cover with aluminum foil lightly coated with cooking spray.
Bake until heated through and cheese is melted, about 25 minutes. Remove foil and bake until bubbly, 5 to 10 minutes.
Top with avocado, cilantro, and/or jalapeño slices, if desired.
