Preheat the oven to 400˚. Bake the potatoes directly on the middle rack until easily pierced with a knife, 45 to 50 minutes. Remove from the oven and let cool 5 minutes.
Meanwhile, melt 3 tablespoons butter in a large skillet over medium heat. Add the onions, shallots, thyme, 1/2 teaspoon salt and a few grinds of pepper. Cook, stirring often, until the onions and shallots are soft and golden, about 15 minutes.
Add the red wine to the skillet and cook until reduced, about 1 minute. Increase the heat to high and add the beef broth and Worcestershire sauce; cook until the liquid is reduced and the onions are glazed, 6 to 7 minutes.
Halve the potatoes lengthwise. Holding each potato with a kitchen towel, scoop the flesh into a large bowl, leaving a 1/4-inch-thick shell. Add the remaining 4 tablespoons butter and the half-and-half to the bowl and mash until smooth. Stir in half of the onion mixture, 1 cup gruyere and ¼ cup parmesan; thin with more half-and-half if needed. Season with salt and pepper.
Brush the potato skins with melted butter; season the insides with salt and pepper. Set on a baking sheet. Mound the potato filling into the potato skins and top with the remaining onion mixture, 1/2 cup gruyere and 2 tablespoons parmesan. Bake until the filling starts browning and the skins are crisp, 18 to 20 minutes. Top with chopped chives.