Set Instant Pot to Sauté function, Normal mode. Add ¼ cup unsalted butter to Instant Pot and stir occasionally until butter has melted completely.
Once butter has melted, add 3 pounds yellow onions (sliced), 3 cloves garlic (minced), 2 sprigs fresh thyme, and 1 bay leaf to Instant Pot. Sauté aromatics, stirring often, 15 minutes.
After 15 minutes, sprinkle 1 pinch sugar and 1 teaspoon salt over aromatics. Stir to incorporate. Continue sautéing, stirring frequently, 15 to 20 minutes or until onions have caramelized.
Once onions have caramelized, pour ½ cup dry red wine into Instant Pot. Stir to incorporate wine, making sure to scrape up any browned bits of garlic or onion that may have stuck to bottom of Instant Pot insert. Simmer ingredients 10 minutes or until majority of red wine has evaporated.
Add 8 cups low-sodium beef broth to Instant Pot and stir to incorporate.
Secure lid on Instant Pot with vent in Sealing position. Set Instant Pot to Manual High Pressure with 5 minute cook time. Instant Pot will pressurize, then cook time will begin.
Toward end of cook time, preheat broiler on High. Position oven racks as needed so ramekins will sit 6 to 10 inches below heating element. Place ramekins on baking sheet and set aside.
When 5-minute cook time ends, immediately Quick Release internal pressure, then carefully remove lid. Use caution - any escaping steam will be extremely hot.
Taste soup and adjust salt if needed. Transfer soup from Instant Pot into ramekins, dividing soup evenly between each ramekin. Remove and discard bay leaf.
Tear 1 slice French bread into large pieces. Top 1 ramekin of soup with pieces of French bread, letting bread rest on top of soup. Repeat until all 6 slices French bread have been placed on top of all 6 ramekins. Divide 1 cup shredded fresh Gruyère into 6 equal portions and sprinkle one portion on top of each layer of bread.
Place baking sheet under preheated broiler. Broil soup 1 to 2 minutes or until Gruyère is melted and bubbly, and French bread is golden brown.
When soup is ready, carefully remove baking sheet from oven. Let ramekins stand 2 to 3 minutes then serve immediately while soup is hot.