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Step 1
Melt 4 Tbsp. unsalted butter, cut into pieces, in a medium deep skillet over medium heat. Cook 1 large onion, finely chopped, stirring often, until tender and translucent, 8–12 minutes. Increase heat to medium-high and continue to cook, stirring often, until onion is pale golden brown, 5–8 minutes more.
Step 2
Reduce heat to medium and add 6 garlic cloves, finely chopped, and 1½ tsp. ground cumin to skillet. Cook, stirring, until garlic is fragrant, about 1 minute. Add 3 canned chipotle chiles in adobo, finely chopped, two 15-oz. cans pinto beans, rinsed, and 1 Tbsp. Diamond Crystal or 1¾ tsp. Morton kosher salt. Pour in 1 cup water and bring to a simmer, mashing beans with a potato masher (or a fork and some elbow grease) until mostly smooth. Cook, stirring often, until most of liquid is absorbed, about 2 minutes. (Beans should be risotto-like in consistency, loose enough to fall off a spoon.) Remove from heat and stir in 1 Tbsp. apple cider vinegar. Cover and keep warm.Do ahead: Beans can be made 3 days ahead. Let cool; cover and chill. Reheat over medium-low, thinning with water and seasoning with salt as needed.
Step 3
Whisk 2 tsp. adobo from a can of chipotle chiles in adobo, ½ tsp. ground cumin, ¼ tsp. Diamond Crystal or Morton kosher salt, and ½ cup water in a small saucepan and bring to a simmer over medium heat. Add 4 oz. yellow American cheese, coarsely grated or torn if using singles (about 1 cup), and cook, whisking vigorously, just until cheese is melted and mixture is smooth, about 1 minute. Remove from heat and add 3 oz. Monterey Jack or pepper Jack cheese, coarsely grated (about ¾ cup); whisk until cheese is melted and queso is smooth (return to low heat briefly if needed).
Step 4
Using your hands to avoid bruising, toss 2 ripe avocados, cut into ¼" pieces, with 1 Tbsp. fresh lime juice and a large pinch of salt in a medium bowl.
Step 5
Uncover beans and pour queso over. Top with ¼ cup sour cream, followed by ½ cup good-quality salsa, avocados, and ¼ cup sliced pickled jalapeños. Scatter 4 scallions, green parts only, thinly sliced, and ¼ cup (packed) coarsely chopped cilantro over.
Step 6
Serve dip warm in skillet with tortilla chips and lime wedges.