Place the potatoes in a large pot with 1 teaspoon of salt, cover with an inch of cold water and bring to a boil. Reduce heat to a simmer and cook the potatoes until fork tender, 15 to 18 minutes. Drain, then mash with vegan butter, nutritional yeast and ½ teaspoon pepper. Set aside off of the heat on top of the stove top to keep warm.
In a large, oven safe skillet, heat olive oil over medium heat. Add the onion, carrot and celery and cook for 5 to 7 minutes, or until the vegetables start to soften. Add the thyme and tomato paste and cook for 1 to 2 minutes, stirring to coat all of the vegetables.
Preheat the oven to 425˚F. Add the lentils, diced tomatoes and stock and bring to a boil. Reduce heat to a simmer and cook covered for about 20 minutes, or until the lentils are tender, and most of the liquid is absorbed. Season with remaining ½ teaspoon of salt and pepper. Add the peas and soy sauce and cook for 1 to 2 minutes. Remove from heat.
Add the mashed potatoes on top of the lentil mixture, smoothing them into a single layer. Place the skillet on a rimmed sheet pan (to catch any drips) and bake for about 25 minutes, or until the potatoes become lightly golden. Let cool slightly before serving.