Preheat the oven to 375°F. Grease an 11 x 8" baking dish and set aside.
Blister the two jalapeños over the open flame of a burner until charred all over. If you don't have a gas stove, place the jalapeños on a baking sheet lined with parchment paper and place it under the broiler. Broil until the skin blisters and turns black. Turn the peppers over and continue to broil on the other side. Set the jalapeños aside to cool.
Once the peppers are cool, remove the stems and place them in a large food processor, and blitz until smooth. ** Transfer the peppers to a plate and set aside.
Heat the olive oil in a large cast-iron skillet over medium heat until shimmering. Add the shallots and sauté until just translucent. Add the garlic and sauté until fragrant, about 30 seconds more.
Add the beans, veggie stock, spices, half of the salt, and honey to the skillet. Bring the mixture to a boil and reduce to a simmer. Let cook until most of the liquid is absorbed about 15-20 minutes.
While the beans are simmering make the bechamel. In a small saucepan, melt the butter over medium heat until frothy. Stir in the flour to form a roux. Whisk the milk into the roux slowly until a smooth sauce forms. Stir in the remaining salt and cook until bubbles break the surface.
Reduce the heat to low and add the goat cheese, stirring until it melts and becomes fully integrated. Add the jalapeños and cook for 5 minutes more. Take the sauce off of the heat and stir in the yogurt. Cover the sauce and set aside.
Ladle a little of the bechamel into the prepared baking dish. Spread the sauce with the back of the ladle to create a thin, even layer.
Stack and wrap 4 corn tortillas in a damp paper towel. Place the bundle in the microwave and heat for 30 seconds. Working quickly, spoon and spread a little of the sauce in the center of the tortilla. Add a couple of spoonfuls of the beans and cover with a sprinkling of the mozzarella cheese. Fold the tortilla closed and place it in the baking dish, seam-side-down. Repeat with the remaining hot tortillas.
Repeat all of the steps above with another 4 tortillas and repeat again with the remaining 4 tortillas. I work in batches of 4 because this is the number of tortillas I can comfortably fill before they cool down too much. ***
Once all the tortillas are filled and nestled into the baking dish, cover them with the remaining cream sauce and a sprinkling of mozzarella. Transfer the dish to the oven and bake until the cheese melts and bubbles. This should take about 15 minutes. Turn on the broiler and broil the enchiladas until the cheese is golden, about 5 minutes more but be sure to keep an eye on it.
Take the enchiladas out of the oven and let sit for 10 minutes before serving. When ready to serve, cover the enchiladas with avocado and cilantro and serve alongside the pickled onions.