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Preheat oven to 375 degrees F (190 degrees C). Process cubed bread in a food processor to make bread crumbs. Set aside. Heat olive oil in a deep ovenproof skillet or Dutch oven. Add onion; cook and stir until softened, about 5 minutes. Add garlic; cook and stir until fragrant, about 1 minute. Add quinoa, chicken stock, and water to the skillet. Bring to a simmer; cover and cook until quinoa is tender, about 10 minutes. Heat 1/4 cup butter in a saucepan over medium-low heat. Add flour; cook and stir to form a paste, about 2 minutes. Slowly whisk in skim milk. Season with salt and ground black pepper; simmer on low until thickened, about 5 minutes. Remove saucepan from heat; stir in Cheddar and mozzarella cheeses, a little at a time, until combined. Stir cheese sauce into quinoa mixture in the skillet. Melt 1 tablespoon butter in a separate skillet over medium heat. Add bread crumbs; cook and stir until crumbs are toasted, about 2 minutes. Place tomato slices on top of quinoa; top with bread crumbs. Quinoa mixture will be soupy but will firm up during baking. Bake in the oven until golden brown, about 25 minutes. Allow to rest for 5 minutes before serving.