Preheat your oven to 375°F (190°C). Begin with preparing the mashed potatoes. Cut the Yukon Gold potatoes into evenly sized halves or quarters for uniform cooking. Place the potatoes in a large stockpot and cover them with water, adding about 1 tablespoon of kosher salt. Simmer over medium heat until fork-tender, around 20 to 25 minutes. Drain the water, but reserve 1 cup of the starchy potato water for later.
Meanwhile, prepare the stew filling. In a large heavy-bottomed pot, heat the olive oil over medium heat. Add the diced onions and mushrooms, and sauté for 7 to 8 minutes until aromatic and slightly browned. Add the carrots, parsnips, celery, garlic, thyme, salt, and pepper. Stir well and continue cooking for about 10 minutes, allowing the vegetables to soften and the mushrooms to release their juices. Let the moisture cook off completely.
Deglaze the pan by pouring in the white wine, scraping any flavorful bits from the bottom. Let it simmer gently until the wine reduces and the root vegetables become fork-tender. Add the peas and white beans to the mixture and stir to combine.
Sprinkle the flour over the vegetable mixture and stir constantly for about 2 minutes to cook out the raw flour taste. Gradually add 1 cup of the warm vegetable-miso broth, stirring as the mixture thickens. Slowly incorporate the remaining broth one cup at a time, allowing the stew to simmer and become rich and velvety. Stir in the Dijon mustard and remove from heat. Taste and adjust salt, pepper, or a few drops of apple cider vinegar for added brightness. Fold in the chopped parsley.
Return to the mashed potatoes. Transfer the drained potatoes back to the pot and mash thoroughly with a masher. Add olive oil, sour cream, garlic powder, salt, pepper, and, if using, nutritional yeast and truffle oil. Loosen the consistency by incorporating 1/4 to 1/2 cup of the reserved hot potato water until smooth and creamy.
To assemble the shepherd’s pie, spread the hearty vegetable filling evenly in a greased 9x13-inch baking dish, large cast iron skillet, Dutch oven, or individual ramekins. Spoon or pipe the mashed potatoes over the top, smoothing or decorating as desired. If the potatoes feel too stiff to pipe, add a bit more hot potato water to soften the texture. Drizzle a little extra truffle oil over the top for a final touch.
Place the baking dish on a sheet pan to catch any overflow and bake in the preheated oven for 20 to 30 minutes, until the filling is bubbling and the potato topping is slightly golden and crisp. Garnish with fresh parsley or a sprig of thyme just before serving.