Preheat oven to 425°F. Coat 13-by-9-inch baking dish with nonstick spray.
In large non-stick skillet, heat oil over medium. When oil shimmers, add 1 cups onion and cook, stirring occasionally, until translucent, 2 to 3 minutes. Add mushrooms, zucchini, and 1/4 tsp salt and cook, stirring occasionally, until vegetables are softened, 15 to 20 minutes.
Meanwhile, make sauce: In blender, purée tomatoes, chipotle powder, garlic, chili powder, cumin, oregano, and remaining 1/2 cup onion and 1/2 tsp salt.
Transfer cooked vegetables to medium bowl. Stir in chicken and 1 cup tomato sauce.
Spread 1⁄4 cup tomato sauce in bottom of prepared baking dish. Top with 3 tortillas, overlapping to fit dish. Sprinkle with half of chicken mixture and 1⁄4 cup cheese. Top with 3 more tortillas, remaining chicken mixture, and 1⁄4 cup cheese. Top with remaining 3 tortillas. Spread top with remaining sauce and sprinkle with remaining cheese. Bake until golden and bubbling, 35 to 40 minutes.