Preheat an oven to 400 degrees F (200 degrees C). Heat oil in a large skillet over medium-high heat. Cook the onion and garlic in the oil until tender, about 5 minutes. Stir in zucchini, 1/4 cup diced chiles, 1 teaspoon chili powder, and 1/4 teaspoon black pepper. Cook until softened, 3 to 5 minutes. Remove zucchini mixture from skillet and reserve.
Melt butter in the skillet over medium low heat. Stir in flour, salt, remaining 1 teaspoon chili powder, and 1/8 teaspoon pepper. Cook, stirring, for 1 minute. Pour in milk; whisk until thickened, 3 to 5 minutes. Stir in the remaining 1/4 cup of diced chiles and 1 cup of Monterey Jack cheese.
Stir 1/2 cup of cheese sauce into the zucchini mixture. Spoon 1/3 cup squash mixture down the center of each tortilla; roll up. Place filled tortillas in prepared baking dish, pour remaining cheese sauce over. Cover and bake in preheated oven until hot, about 25 minutes. Remove from oven; sprinkle with remaining 1/2 cup Monterey Jack cheese and the chopped tomatoes.
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