Using a potato ricer or a food mill, process the butternut squash and potatoes separately. In a large bowl, mix squash and potato with a wooden spoon. Add oil and 1 teaspoon sea salt to the bowl and mix. Mix in the flour until just incorporated; do not overmix. As soon as the dough comes together, add the potato starch. Mix thoroughly, make a tight ball, and let it rest in the fridge, covered with plastic wrap, for 1 hour. After the dough has rested, roll the dough to ¾-inch thickness and portion into 1½-inch pieces with a dough scraper or knife.
Set aside the gnocchi on floured parchment paper, wrap in plastic wrap, and freeze until ready to use. Do not thaw before use. To cook, bring well-salted water to a boil, and drop in the frozen gnocchi. The gnocchi will be ready when they start to float, about 2–3 minutes.
Toast the farro in a dry pan until fragrant, about 2–3 minutes. Make a sachet with the lemon thyme, whole fennel seeds, garlic, and peppercorns, by placing the ingredients in a piece of cheesecloth, and tying off the cheesecloth with a piece of butcher’s twine. Boil the farro, ancho chili, and the sachet in salted water. If foam rises to the top of the water, skim it off. Once the farro is al dente, about 13 minutes, strain the grains from the water and cool. Heat the olive oil in a pan over medium-high heat. Sauté the onion and fennel with the ground cumin and ground fennel seeds until translucent and fragrant. Add red bell pepper and cook for an additional 2 minutes. Mix in the al-dente farro. Add white wine and vegetable stock and reduce by 75 percent. Add butternut squash and stir. Cook until the flavors develop and the sauce thickens.