In a large soup pot, heat 2 tablespoons of the olive oil over medium heat. Add the sliced onions to the pot. You should hear a decent sizzle. Sauté until the onions are just starting to soften, about 3 minutes. Lower the heat. Slowly cook the onions until they are light brown, slightly jammy, and sweet, stirring frequently. This should take about 60 minutes. Add a splash of water to the pot if the onions start to dry up or burn.
Scoop 1/3 cup of the cooked onions out of the pot and set aside.
Increase the heat back to medium. Add the thyme, bay leaf, lentils, and tomato paste to the pot. Stir to combine. Add the balsamic vinegar and tamari, and use your spoon to scrape up any browned bits from the bottom of the pot. Season the mixture with salt and pepper, and then add the vegetable stock. Cover and bring to a boil. Lower the heat to a simmer, and cook until the lentils are tender, about 20 to 25 minutes.
Remove the bay leaf from the pot and discard. Divide the French onion lentil stew among four 1-cup ramekins. Place the filled ramekins on a baking sheet.
Preheat the broiler to high.
In a blender, combine the reserved cooked onions, remaining 1 teaspoon of olive oil, nutritional yeast, almond milk, salt, and pepper. Whiz on high until you have a chunky paste.
Spread the onion cream thinly over the baguette slices. Place 2 baguette slices over each pot of lentils.
Slide the French onion lentil pots under the broiler, and cook until the edges of the bread are crisp and browned, about 1 minute. Serve hot.