Toss the pork with ½ teaspoon each salt and pepper. In a 12-inch skillet over medium-high, heat the oil until barely smoking. Add the pork and cook, stirring occasionally, until browned all over, 6 to 8 minutes. Using a slotted spoon, transfer to a medium bowl; set aside.

To the same skillet over medium-high, add the chopped onion and bell pepper. Cook, stirring occasionally, until softened and beginning to brown, 3 to 4 minutes. Add the garlic, habanero and cumin; cook, stirring, until fragrant, about 30 seconds. Stir in 3 cups water and ¼ teaspoon salt, scraping up any browned bits.

Return the pork and any accumulated juices to the pan, stir to combine and bring to a simmer. Cover, reduce to medium-low and simmer until a skewer inserted into a piece of pork meets no resistance, about 1 hour. Meanwhile, in a small bowl, stir together the sliced onion, the Fresno chilies, cilantro, lime juice and ¼ teaspoon salt. Cover and refrigerate until ready to serve.

When the pork is tender, stir in the quinoa. Return to a simmer and re-cover. Cook, stirring occasionally and adjusting the heat as needed to maintain a simmer, until the quinoa is tender and most of the liquid has been absorbed but the mixture is creamy and saucy, 12 to 15 minutes.

Remove the skillet from the heat and let stand, covered, for about 10 minutes. Taste and season with salt and pepper. Serve topped with some of the onion-chili mixture and offer the remainder on the side.