Preheat oven to 350°. Coat the outside of six 6-oz. custard cups with nonstick spray.
Brush both sides of tortillas with 1 Tbsp. oil; season with salt.
Line 6 cups of a jumbo muffin tin with tortillas; press prepared custard cups inside to set the shape.
Bake tortilla cups until beginning to brown, 20 minutes, rotating halfway through.
Remove muffin tin from oven; increase temperature to 425°.
Meanwhile, sweat onion and poblano in remaining 2 Tbsp. oil in a saucepan over medium heat until softened, about 10 minutes.
Stir in garlic and oregano; cook until fragrant, 1 minute.
Add tomatillos; cook until they begin to release their liquid.
Add pinto beans, black beans, and broth.
Cook and mash beans and tomatillos with a potato masher until fairly smooth; stir in zest and season with salt.
Remove custard cups from tortilla cups.
Scoop ½ cup bean mixture into each tortilla cup; top each with 2 Tbsp. cheese and bake until cheese melts, 5 minutes.
Crack an egg into each tortilla cup; bake until egg whites are set, 15 minutes.
Top Huevos Rancheros Cups with avocado and serve with Pico de Gallo Verde.
