Arrange tomatoes on a pyrex baking dish, cut sides up along with whole garlic cloves and sliced red onion. Drizzle with oil; season with salt and pepper. Scatter 2 tablespoons Parmesan cheese and 2 tablespoons basil evenly over top. Roast until tomatoes are juicy and bubbling, about 20 minutes; set aside.
Meanwhile, bring large pot of salted water to boil. Add rotini and cook according to package directions until al dente. Drain and transfer to a large bowl.
Grate zucchini and yellow squash. Add grated squash, lemon juice, lemon zest and remaining Parmesan cheese and basil to pasta. Toss and combine. Season to taste with salt and pepper.
Top pasta with roasted tomatoes, garlic and onion and serve!