Preheat the oven to 475°F. Line a rimmed baking sheet with parchment paper.
Cook the penne pasta according to the package directions, omitting the salt and fat. Drain and set aside.
Combine the squash and the next 7 ingredients (through garlic) in a large bowl; toss well to coat. Arrange the vegetables in a single layer on the prepared baking sheet. Bake for 20 minutes or until browned, stirring after 10 minutes. Drizzle the vinegar over the vegetables; toss well.
In a large bowl, combine the hot pasta, vegetable mixture, goat cheese, basil and thyme, and toss well. Serve!