THE SALSA: Heat the canola oil in a medium skillet over moderate heat. Cook the onions until soft, about 10 minutes. Transfer to a food processor fitted with the metal blade or a blender.
Add the remaining ingredients and puree, in batches if you are using a blender, until smooth. Pour into a saucepan. Bring to a boil, reduce to a simmer, and cook, uncovered, 20 minutes. Adjust the seasonings, if needed.
Salsa can be stored in the refrigerator 2 to 3 days, or in the freezer for weeks.
THE SOUP: Heat the olive oil in a large stockpot or saucepan over medium-low heat. Add the onions and cook slowly, stirring frequently, until golden brown and caramelized, about 40 minutes. Add the garlic and cook 10 minutes longer.
Add 3 cups of the Red Tomato Salsa, the chicken broth, chipotle chili, and salt. Bring to a boil, reduce to a simmer, and cook, uncovered, 20 minutes. Stir in the fried tortilla chips and simmer about 10 minutes longer, or just until the chips soften. Remove and discard the whole chipotle chili.
TO FINISH: Ladle soup into bowls and top each with some of the garnishes: chopped cilantro, a few chunks of avocado and panela, a dollop of crema fresca, and a lime wedge. Serve hot.