In a medium bowl, whisk together coconut aminos, beef broth, keto-friendly sweetener, minced garlic, grated ginger, sesame oil, and red pepper flakes (if using).
Place the short ribs in a large dish or resealable bag. Pour the marinade over the ribs, ensuring they are well coated. Cover and refrigerate for at least 4 hours, or preferably overnight.
Preheat your oven to 300°F (150°C). Remove ribs from the marinade, reserving the marinade. Place the ribs in a single layer in a large Dutch oven or oven-safe pot with a lid.
Pour the reserved marinade over the ribs. Add enough water or beef broth to come halfway up the sides of the ribs. Bring to a simmer on the stovetop.
Cover the Dutch oven tightly and transfer to the preheated oven. Braise for 2.5 to 3 hours, or until the ribs are fork-tender and easily pull away from the bone.
Carefully remove the ribs from the pot and set aside. Skim off any excess fat from the sauce. In a small bowl, whisk the xanthan gum into a tablespoon of the hot sauce until smooth, then whisk this mixture back into the main sauce in the pot. Bring the sauce to a gentle simmer on the stovetop, stirring constantly, until it thickens to your desired consistency.
Return the short ribs to the thickened sauce to warm through. Garnish with sliced green onions before serving.