Bring a large skillet or saucepan over medium-heat and add olive oil, mushrooms, onions, and salt. Mix well and cook for 10 minutes, stirring occasionally to encourage browning, until slightly caramelized and juicy.
Add the flour and mix well. Cook for about 5 additional minutes, toasting the flour until lightly brown. Add the vegan butter (if using), along with the the garlic, thyme, sage, garlic powder, onion powder, red pepper flakes (if using), black pepper and nutritional yeast and cook 2-3 minutes to toast spices and cook the garlic.
Add the red wine and cook for 1 minute to cook off the alcohol. Then pour in 5 cups of water, rice vinegar, tamari, bouillon paste, and miso. Mix well, turn the heat up to high, and bring to a simmer. While at a simmer, cook for about 5 minutes. Then, reduce the heat to medium and continue to cook for an additional 5-10 minutes until the gravy is thick and saucy (or until desired consistency is reached!). Serve over everything!
For a smooth gravy, remove from heat and transfer to a blender. Blend until smooth and transfer back to the skillet. Cook for a few minutes, until smooth and creamy, and serve. If making ahead, store in the fridge.