Preheat the oven to 400°F (200°C). Have ready 2 rimmed baking sheets.
On 1 baking sheet, combine the chopped fennel, squash, onion, and garlic. Add 2 tablespoons of the oil and toss to coat. Add the thyme and ½ teaspoon salt and toss again. Transfer half of the mixture to the second baking sheet. Roast both pans for 15 minutes, then stir the vegetables. Reverse the position of the pans in the oven and roast until the vegetables are tender and lightly browned, about 15 minutes more. Cool on racks.
Meanwhile, bring a large pot of salted water to a boil. Add the penne and cook until al dente according to package instructions; drain. Chop enough of the reserved fennel fronds to measure about ½ cup (3/4 oz/20 g).
In the empty pasta pot, combine the penne, roasted vegetables, tomatoes, olives, chickpeas, basil, fennel fronds, and the remaining 2 tablespoons oil. Toss to mix.
Divide the pasta and vegetables among bowls and serve right away, sprinkled with nutritional yeast, if desired.