Preheat the oven to 400°F (200°C). Line a baking sheet with parchment paper and lightly grease it.
Dice the butternut squash, Brussels sprouts, and apple into bite-sized pieces.
Place the butternut squash and Brussels sprouts on the prepared baking sheet. Add olive oil, thyme, salt, and black pepper, then toss until evenly coated.
Roast for about 20 minutes. Move the vegetables to one side of the pan and add the diced apples.
Continue roasting for 10–15 minutes, or until the vegetables are fork-tender and lightly caramelized.
While the vegetables roast, bring a large pot of salted water to a boil. Cook the rotini according to the package directions. For al dente pasta, cook it 1–2 minutes less than the recommended time.
Drain the pasta, reserving about 1 tablespoon of pasta water. Toss the pasta with a small drizzle of olive oil or the reserved pasta water and allow it to cool.
While the pasta cooks, prepare the dressing. Whisk the olive oil, balsamic vinegar, Dijon mustard, maple syrup, garlic, salt, and black pepper together until smooth and emulsified.
Allow the roasted vegetables and apples to cool slightly.
Add the cooled pasta, roasted vegetables, apples, goat cheese, and dried cranberries to a large bowl.
Pour the maple Dijon dressing over the salad and gently toss until everything is evenly coated.
Serve immediately or refrigerate until ready to serve. For the best texture when preparing this fall pasta salad ahead, add the goat cheese and dressing shortly before serving.