Preheat oven to 400 degrees F (200 degrees C). Line a baking sheet with parchment paper. Arrange butternut squash into a single layer over the prepared pan. Drizzle with 2 tablespoons olive oil and season with salt and pepper. Bake squash in the preheated oven, turning halfway, until browned and softened, about 35 minutes. Heat the remaining 2 tablespoons olive oil in a large skillet over medium heat. Add zucchini, garlic, Italian seasoning, red pepper flakes, salt, and pepper. Cook and stir until zucchini is tender, about 4 minutes. Mix in baked squash and lemon juice until just combined. Top with Parmesan cheese.