Bring a large pot of well-salted water to a boil over high heat. Preheat the oven to 375°F, butter a casserole dish, and line a baking sheet with foil or parchment.
Remove the bottoms of the chard stems from just below the leaf, and reserve for another use (see below note). Slice the leaves horizontally into one-inch wide ribbons, and add to the boiling water. Reduce to a simmer and cook for 5 minutes, or until well wilted. (You may need to do this in batches.) Strain, and when cool enough to handle, squeeze as much water out as possible. Set aside.
Slice the tomatoes in half, toss in one teaspoon olive oil, and sprinkle with ¼ teaspoon salt and a light flourish of pepper. Spread the tomatoes on the baking sheet, their cut sides facing up. Roast for 20 minutes, or until slightly dried and puckered around the edges.
Add the remaining tablespoon of olive oil to a sauté pan over medium heat, and sauté the onion until soft, about 10 minutes. Stir in the garlic and cook an additional minute.
In a large mixing bowl, whisk together the cheeses, milk, eggs, salt, pepper, and nutmeg until well combined. Fold in the chard, tomatoes, cooked quinoa, and sautéed onions, and scrape into a casserole dish using a spatula. Bake for 30 minutes, or until bubbling.
Melt the butter in the sauté pan and add the breadcrumbs and pine nuts. Sauté until lightly toasted, about two minutes. Spread across the top of the baked casserole. Add a little Parmesan cheese for garnish on top.
Serve warm with a fresh green salad.