Melt butter substitute over medium heat. Add onions and cook, stirring occasionally and scraping up any brown bits from the bottom of the pan, until caramelized, about 45-50 minutes.
Bring 5 quarts of water to a full rolling boil.
Combine 1 quart of cool tap water and 1 package of Gravy Mix in a separate container. Mix with a wire whisk until lump-free.
Pour the water and Gravy Mix blend into boiling water.
Stir until gravy returns to a boil. Simmer for 1 minute while stirring constantly.
Remove from heat and stir in caramelized onions. Pour soup into serving container and maintain internal gravy temperature at 165°F during service.
Pour soup into 8 oz. heat-proof soup bowls. Garnish with 2 slices of toasted bread and sprinkle with 1 oz. of cheese. Broil until cheese is melted and light golden-brown. Garnish with thyme.