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Position rack in upper third of oven; preheat to 450 degrees F.
Place squash halves cut-side down in a microwave-safe dish and add water. Microwave, uncovered, on High until the flesh is tender, 10 to 12 minutes. (Alternatively, place squash cut-side down on a large rimmed baking sheet. Bake at 400 degrees F until tender, 40 to 50 minutes.)
Meanwhile, heat oil in a large skillet over medium heat. Add onion and garlic; cook, stirring, until starting to soften, 3 to 4 minutes. Add mushrooms and bell pepper and cook, stirring, until the vegetables are tender, about 5 minutes more. Add tomatoes, Italian seasoning, 1/4 teaspoon pepper, crushed red pepper and 1/8 teaspoon salt. Cook until heated through and the flavors have blended, about 2 minutes. Remove from heat and stir in all but 10 or 12 pepperoni halves. Cover and reserve.
Use a fork to scrape the squash from the shells into a large bowl, being careful to keep the shells intact. Stir in 1/4 cup mozzarella, Parmesan and the remaining 1/4 teaspoon pepper and 1/8 teaspoon salt. Add the tomato mixture to the bowl; stir well to coat. Place the squash shells, cut-side up, on a rimmed baking sheet. Divide the filling between the halves. Sprinkle with the remaining 3/4 cup mozzarella and arrange the reserved pepperoni on top.
Bake until the filling is hot and the cheese is melted, about 15 minutes. Turn the broiler to high and broil, watching carefully, until the cheese and pepperoni start to brown, 1 to 2 minutes. Cut each boat in half to serve.