Bring a large pot of salted water to a boil. Cook the noodles according to package directions until just tender. Reserve ½ cup of the cooking water before draining.
While the noodles cook, melt the butter in a large skillet over medium heat. Add the garlic and cook for 1–2 minutes, stirring frequently, until fragrant but not browned.
Whisk in the San-J Tamari, honey, sesame oil, and red pepper flakes. Simmer for about 1 minute.
Add the drained noodles to the skillet and toss until evenly coated. Add a splash of the reserved noodle water as needed to create a silky sauce that clings to the noodles.
Stir in most of the green onions and season with black pepper to taste.
Transfer to a serving platter or bowls and garnish with the remaining green onions and sesame seeds.
Serve immediately with lime wedges for squeezing over the top.