Set cooker to sauté mode. Add coconut oil, heat until melted and hot.
Add 1 cup red onion and garlic. Stir until onion is translucent, about 2 minutes.
Add cumin, coriander, and chili powder. Stir and cook 30 seconds.
Stir in chipotle pepper and adobo sauce, vinegar, crushed tomato, broth, and beans. Stir to mix all ingredients.
Set cooker to pressure cook mode on high for 40 minutes.
While soup is cooking, prepare pickled onions. Put remaining 1 cup red onions in a 1 pint canning jar (like Mason or Weck).
In a small saucepan, combine water, vinegar, sugar, and salt. Bring to a simmer and pour over onions in canning jar.
Let cool, use some for soup toppings and cover and refrigerate the rest for later.
When the soup in the cooker is finished, let the pressure release naturally for at least 5 minutes before using the instant release button. When pressure has been released, uncover, and stir in salt and pepper.
Ladle soup into serving bowls. I recommend topping with the pickled onions, avocado, coconut yogurt, pumpkin seeds, cilantro, and wedges of lime.