Preheat an oven to 400°F. Pierce the potatoes with a fork several times. Transfer them to the oven and bake for 1 hour. Cut them in half lengthwise and let cool for 10 minutes.
While they are baking, melt 2 tablespoons of the vegan butter in a saute pan over medium heat. Add the onion and cook, stirring frequently, until it just starts to brown, about 6 minutes. Add the bell pepper and cook, stirring frequently, for another 4 to 5 minutes. Remove from the heat and set aside.
Scoop out most of the potato flesh into a mixing bowl. Combine this with the onion-pepper mix, melted Earth Balance from the saute pan, the grated Daiya, the Better Than Sour Cream, and the salt and pepper, mixing well.
Line a large baking sheet with foil. Place the potato skins scooped-outside-down onto the baking sheet. In a small pan, melt the remaining 1 tablespoon of Earth Balance and brush it onto the potato skins. Sprinkle salt, pepper, and garlic powder on them. Flip them over and fill with the potato/Daiya/onion-pepper mix. Top each potato with the grated Daiya.
Bake for 15 to 20 minutes.
Garnish each potato with chopped chives, if using.