Heat the oven to 250°F. Wrap the tortillas in aluminum foil and warm in the oven.
Meanwhile, in a small bowl toss the tomatoes with 1 Tbs. of the lime juice, about 1-1/2 Tbs. of the cilantro, and a generous pinch of salt. Set aside.
If using the pepitas, heat 1 Tbs. of the olive oil and the pepitas in a 12-inch skillet over medium heat. Cook, stirring frequently, until they are puffed and some are golden brown, 1 to 2 minutes. Using a slotted spoon, transfer the pepitas to a plate lined with a paper towel. Sprinkle with a generous pinch of salt and toss.
Return the pan to medium heat. Add the remaining 1 Tbs. olive oil. (Or if not using pepitas, heat the 2 Tbs. oil over medium heat.) Add the chipotle, adobo sauce, and cumin. Stir to blend into the oil, and then add the beans and 2 Tbs. water to the pan, stirring to blend. Simmer until warmed through, about 2 minutes. Reduce heat to low. Mash about half of the beans with a fork. Stir in the cheddar and the remaining 2-1/2 Tbs. cilantro and 1 Tbs. lime juice. Season to taste with salt. If the beans seem too thick, add a tablespoon or two of water to thin to a soft, spreadable consistency.
Working with one tortilla at a time, spread about 1/4 of the beans along the bottom third of a tortilla. Top with 1/4 of the spinach, and sprinkle with about 1/4 of the tomatoes and pepitas (if using). If you like, add a little lime juice and sour cream on top. Fold the bottom edge over the filling, fold in the sides, and roll up the burrito.