Preheat the oven to 375 degrees F. Generously grease a 12-cup muffin tin with the 1 tablespoon butter.
Combine the potatoes, 4 tablespoons melted butter, garlic powder, thyme, 1 teaspoon kosher salt and 1/2 teaspoon black pepper in a large bowl. Gently toss the potatoes with your hands until fully coated with the butter and herbs. Layer the potatoes in the prepared muffin tin. Tuck 2 onion slices into each potato stack. Bake until the potatoes are easily pierced with a knife and the edges are golden brown, 50 to 60 minutes. Sprinkle with 1/2 teaspoon flaky sea salt and 1/2 teaspoon pepper.