Preheat oven to 375° F. Place the butternut squash onto a sheet pan in a single layer and drizzle with 2 tablespoons olive oil. Sprinkle with kosher salt and freshly ground pepper. Toss to coat and roast for 30-35 minutes, until squash is tender and lightly browned.
In a medium saucepan, bring farro, apple cider, 1/2 teaspoon salt, bay leaves, garlic and 2 cups water to a simmer. Simmer uncovered, until farro is tender but still has some chew and liquid evaporates, about 30 minutes. If all the liquid evaporates before the farro is done, add a little more water. Let farro cool, then discard bay leaves and garlic clove.
In a large bowl, whisk together olive oil, lemon juice and a pinch of salt. Add the farro, squash and scallions and mix well. This salad base will keep for up to 4 hours at room temperature or overnight in the refrigerator (bring to room temperature before serving). Just before serving, fold in arugula, nuts and the cheese. Sprinkle flaky salt to taste.