Preheat the oven to 375 degrees F. Place the bacon on a baking rack set on a sheet pan and bake it for 20 to 30 minutes, until browned (it won't be crisp). Cut the bacon in very large dice.
Meanwhile, in a small (9-inch) Dutch oven, such as Le Creuset, heat the olive oil and butter over medium heat. Add the onion and cook for 6 to 8 minutes, until tender and starting to brown. Add the thyme, 2 teaspoons salt and 1 teaspoon pepper and cook for 1 minute. Add the farro and chicken stock and bring to a simmer. Place the squash on top of the farro mixture, cover, and bake in the same oven with the bacon for 30 minutes, until the squash and farro are tender. Check once during cooking and add a little chicken stock if it's dry.
Sprinkle the bacon and parmesan on the squash and farro and bake uncovered for 15 to 20 minutes, until most of the liquid evaporates, the farro and butternut squash are tender, and the cheese has melted. Serve hot directly from the pot.
Make it ahead: Assemble the dish, including the bacon and parmesan, and refrigerate for up to 2 days. Bake before serving.