Peel and slice the onions thinly. In a large skillet over medium high heat, heat the olive oil. Add the sliced onions, salt and pepper. Stir and cook until the onions start to soften, about 5 minutes. Add the grated apple tossing to coat and add ¼ cup of water. Reduce the heat to medium, cook until the onions are very soft and deeply caramelized, about 25 minutes, stirring occasionally (you may have to adjust the heat to keep from burning). Add the vinegar and increase the heat, stirring until the liquid has all been evaporated. Stir in the thyme. Remove from the heat and let cool. Remove about 1 tablespoon of the caramelized onions for garnish if desired and set aside.
In a large mixing bowl, whisk together the Vegenaise and Vegan Gourmet until smooth. Stir in the caramelized onions and some hot sauce. Taste and adjust seasoning if needed. Cover with plastic wrap and refrigerate for at least 1 hour or up to a day or two ahead. Top with the reserved onions and serve with chips or cut up vegetables for a perfect gluten free dip.