Bake the potatoes: Preheat the oven to 375°F (190°C). Scrub the potatoes, pierce them a few times with a fork, and bake them directly on the rack for about 60 minutes, until a knife slides in easily.
Cook the Filling: In a large pan, sauté the meatless crumbles, onion, green pepper, and red pepper over medium heat until softened. Add garlic and cook for 30 seconds more. Stir in mixed vegetables, miso paste, ketchup, and all seasonings. Cook until it's hot and slightly thickened.
Prepare the Potato Shells: Let potatoes cool just enough to handle. Slice each in half lengthwise and gently scoop out the centers, leaving a thin wall so the skins stay sturdy.
Make the Mashed Topping: Mash the scooped potato with dairy-free butter, vegan sour cream, vegan cream cheese, dairy-free milk, shredded cheese, nutritional yeast, and parsley. Add the milk gradually until smooth and fluffy.
Fill The Potatoes: Spoon the shepherd’s pie filling into each shell, then top with the mashed potatoes. Lightly press so the topping stays in place.
Bake Again: Return to the oven and bake for 20 minutes at 375°F (190°C) until heated through.
Finish With Cheese: Sprinkle a little extra dairy-free cheese on top and bake for 5 more minutes until melted.