Preheat the oven to 375°F (190°C). Line a baking sheet with parchment paper and lightly grease it with olive oil. In a mixing bowl, combine the onions, garlic, vegan mince, thyme, allspice, black pepper, mushroom powder, crushed red pepper flakes, miso paste, parsley, dijon mustard, and panko breadcrumbs. Mix until the ingredients are evenly mixed and the meat is firmer feeling from the breadcrumbs binding it.
Form the mixture into meatballs roughly 1 ½ inches (4 cm) in diameter and arrange them evenly on the prepared baking sheet. Drizzle lightly with the remaining olive oil, and roll the balls around the tray so that they are coated all over.
Bake for 18 minutes, turning once halfway through, until firm and browned all around.
While the meatballs bake, prepare the gravy. Melt the vegan butter in a saucepan over medium heat. After 90 seconds, when the butter is hot and bubbling, add the flour and whisk continuously for 2 minutes to create a roux.
Add the nutmeg, oregano, and black pepper, whisking briefly to combine.
Gradually pour in the plant-based milk while whisking, then add the vegetable stock and tamari. Continue whisking for 5–6 minutes until the sauce thickens and becomes smooth.
Add the baked meatballs to the pan with the gravy. Spoon the sauce over them and simmer for 5 minutes over low heat until evenly coated and heated through.
Garnish with parsley and minced chives to serve.