Preheat the oven to 325 degrees F.
Heat 1 tablespoon of the olive oil in a large oven-safe Dutch oven or pot over medium-high heat.
Season the beef all over with salt and pepper. Sprinkle the flour over the beef and rub it on both sides.
Place the beef in the skillet and sear it on both sides, about 2 minutes per side. Remove the beef and place it on a plate.
Reduce the temperature under the pot to low and add in the remaining tablespoon of olive oil, and the onions and garlic with another pinch of salt and pepper. Cook for 5 minutes. Stir in the apple cider and cook, stirring often, for another 15 to 20 minutes, until the onions are caramelized.
Place the roast back in the pot, on top of the onions. Add the squash cubes in the pot too. Cover and cook for 2.5 to 3 hours.
After 3 hours, remove the pot from the oven and shred the beef with a fork. Serve the beef with the caramelized onions and butternut squash over the cauliflower rice.