Preheat the oven to 375 degrees . Pierce the squash all over with a fork. Place on a foil-lined baking sheet. Bake until tender when pierced with a knife, about 1 hour 15 minutes.
Meanwhile, make the tomato sauce. In a medium skillet, heat 2 tbsp. EVOO over medium heat. Add the onion, garlic, thyme and crushed red pepper. Cook, stirring occasionally, until the onion softens, about 3 minutes. Stir in the tomatoes, lower the heat to medium-low and simmer for 5 minutes; season with salt and pepper.
Slice the squash in half lengthwise. Using a spoon, remove the seeds. Drag a fork through the flesh, scraping it apart in strands. Transfer the squash to a serving dish; toss with EVOO and season with salt and pepper. Toss with the provolone. Spoon the tomato sauce over the squash. Top with the parmesan and parsley.