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, 15–18 minutes. Drain, then mash with the butter, nutritional yeast, and ½ teaspoon pepper. Set aside, off the heat but on top of the stove to keep warm.
In a large, oven-safe skillet, heat olive oil over medium heat. Add the onion, carrot, and celery and cook until the vegetables start to soften, 5–7 minutes. Add the thyme and tomato paste and cook for 1–2 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 until the lentils are tender and most of the liquid is absorbed, about 20 minutes. Season with remaining ½ teaspoon of salt and pepper. Add the peas and soy sauce and cook for 1–2 minutes. Remove from heat.
Spread 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 until the potatoes are lightly golden, about 25 minutes. Let cool slightly before serving.
Notes
Storage: Store leftovers in an airtight container in the fridge for 3–4 days.