Heat oven to 400º. On a rimmed sheet pan lined with foil, toss together peppers, onion, 1/4 cup oil, 1/2 teaspoon salt and sage, then spread vegetables out in an even layer. Top with thyme sprigs, and roast on the top rack until tender and lightly browned, about 45 minutes, tossing every 15 minutes.
On a separate rimmed sheet pan, toss together beans, tomatoes, 1/4 cup oil, chipotle chile, and adobo sauce, garlic, oregano, 1/2 teaspoon cumin, and salt to taste. Roast on the bottom rack, stirring every 10 minutes, until juices have thickened, 25 to 35 minutes.
Brush tortillas on both sides with oil, then arrange in an even layer on a third rimmed baking sheet (it’s O.K. if the tortillas overlap slightly). Bake until crisp, about 5 to 7 minutes. Immediately sprinkle with salt while they are still hot.
To make the cumin salt, grate the zest from the lime. In a small bowl, stir together lime zest and lime essential oil, 1 1/2 teaspoons salt, and remaining 1/4 teaspoon cumin or a drop or two of Cumin Essential Oil.
To serve, top tortillas with beans, peppers, avocado, queso fresco, and a wedge of fresh lime. Sprinkle with the lime-cumin salt.