Preheat the oven to 375 degrees Fahrenheit/190 degrees Celsius.
Heat two tablespoons of olive oil in a wide skillet or saucepan. Add the thinly sliced onions, a generous pinch of black pepper and salt and cook, stirring frequently, for about 10-12 minutes over medium heat until the onions are nicely caremelized and a rich golden-brown.
Stir in the garlic and saute for a few seconds.
Add the roughly chopped spinach to the skillet and stir for a minute or so until the spinach has wilted. Turn off the heat.
Place the beans and yogurt in a food processor bowl with the nutritional yeast, nutmeg, onion powder or flakes, paprika, if using, two teaspoons of the dried herbs and salt to taste. Add ¾ cup of water (or the bean cooking liquid, if you cooked the beans from scratch). Process until you have a very smooth paste with no graininess--this will take a few minutes depending on how powerful your food processor is. The dip at this point should be a bit runnier than you want the final dish to be because it will thicken up as it bakes.
Add the spinach and caramelized onion mixture to the food processor and pulse a few times. You can choose how chunky or smooth you want the dip to be at this point--pulse just three or four times if you want discernible pieces of onions and spinach in the dip. Or pulse a few more times until everything has broken down and is still discernible but not chunky.
Add half the vegan mozzarella shreds to the food processor and pulse 2-3 times to mix.
In a bowl, mix the remaining mozzarella shreds with the breadcrumbs, the remaining half a teaspoon of herbs, the remaining ½ tablespoon of olive oil and salt and ground black pepper to taste.
Scrape the dip out of the food processor and into a 1 ½ to 2 quart baking dish. Smooth the top.Sprinkle the breadcrumb-cheese mixture evenly over the top.
Place the baking dish into the preheated oven and bake 25 minutes or until the dip is bubbling at the sides. Turn on the broiler for two minutes so the panko-cheeze topping turns golden-brown. Remove the dip from the oven.
Serve hot with vegetable crudites or crackers or wedges of toasted pita bread.