Toss the butternut squash, cauliflower, salt, pepper and nutmeg with 1 tablespoon of olive oil and place on a baking sheet in a single layer. Roast the vegetables, stirring occasionally for even browning, for 20 minutes or until the vegetables are browned and the squash is tender.
Cook the pasta in heavily salted water for 7 minutes or until done. Reserve ¼ cup of the pasta water, drain the pasta and then return to the hot pot.
Melt the dairy free butter substitute in a small, heavy saucepan over medium heat until it starts to brown, about 3 minutes. Add the sage leaves, remove from heat and toss to coat.
Add the roasted vegetables, reserved pasta water, sage leaves and browned butter substitute to the pan with the pasta and toss to coat. Drizzle with the remaining 2 tablespoons of olive oil and additional salt and pepper if desired. Serve immediately.