To make the Chile Relleno: Preheat oven to "broil" and roast the chiles until skin blackens, making sure to turn frequently. Remove chiles from the oven and place into a stainless steel mixing bowl. Peel the outer skin, being careful not to tear the flesh of the chile. With a sharp paring knife, make a long slit the length of each chile and then gently remove and discard all of the seeds. Set the chiles aside while you make the filling.
Heat the oil in a 4 quart saucepan over medium high heat and saute the onion until translucent. Add quinoa and toast for 3 to 5 minutes, stirring constantly. Add salt, pepper, and water to cover about 2 inches over quinoa. Bring to a boil and then reduce heat and simmer, uncovered, until water is absorbed and quinoa is tender. Turn out onto a baking sheet and allow to cool. In a clean pan, saute the mushrooms in butter over high heat. Season lightly with salt and freshly ground black pepper and allow to cool. In a bowl, combine the cooled quinoa and mushrooms with asadero cheese, eggs, thyme leaves, salt and freshly ground black pepper. Stuff each of the chiles with the filling mixture until they are very full and then set aside while you make the sauce.
To make the Asado Sauce: Preheat an oven to 400 degrees F.
Quarter the tomatoes and then place into a stainless steel mixing bowl and combine with the onions, garlic, oil, salt, pepper, and thyme. Turn onto a baking sheet and roast in the preheated oven about 15 to 20 minutes or until the tomatoes and onion start to turn black. Remove from the oven and process mixture in a food processor, working in batches if necessary. In a 4-quart saucepan, combine the processed onion-tomato mixture with the chipotles and heavy cream and heat over medium heat for about 10 minutes. Reduce heat to low and keep the sauce warm until you're ready to serve.
To serve: Preheat an oven to 350 degrees F.
Place the stuffed chiles into the oven and roast for 20 minutes or until heated through. Ladle enough of the warm asado sauce on 4 dinner plates to form large pools and then place 1 chile relleno on each plate and serve.
Handle chiles with latex gloves or with kitchen tongs, avoiding contact with skin or eyes. This vegetarian recipe may be enhanced with shredded cooked meat or poultry; SantaCafe often adds duck confit, which should be added to the quinoa mixture before stuffing the chiles.