Preheat the oven to 350°F. Line a baking sheet with parchment paper. Rub the poblanos with a little bit of oil. Put them on the baking sheet and roast until the skins blister and pucker, 15 to 20 minutes.
Transfer the poblanos to a bowl. Cover the bowl tightly with plastic wrap and let the poblanos steam for 10 minutes.
When the poblanos are cool enough to handle, using your hands, slide off the skins, rinsing the chilies under running water, if necessary, to remove any charred bits. Using a paring knife, cut a vertical slit into each poblano from stem to tip, making an opening large enough for stuffing. Use a spoon to gently remove the seeds and set the poblanos aside.
In a medium skillet over medium heat, whisk together the apple juice, shoyu, mustard and bay leaf. Slide the tempeh into the skillet, bring the liquid to a simmer, reduce the heat to low, and simmer until the liquid is reduced to a few tablespoons, about 20 minutes.
Transfer the tempeh to a paper towel–lined baking sheet to cool. Then crumble the tempeh and set aside.
For the filling:
Heat a medium skillet over medium heat, add 1 tablespoon of oil, and heat until it just starts to shimmer. Add the scallions, carrot, cumin, paprika and salt. Sweat until the carrot begins to soften, stirring occasionally, about 8 minutes. Add the tomato and garlic and cook until the tomato is slightly broken down, 1 to 2 minutes more. Transfer the mixture to a large bowl.
Return the same pan to medium heat, add the remaining 2 tablespoons of oil and the crumbled tempeh. Cook until the tempeh is browned, 8 to 10 minutes. Transfer the tempeh to the bowl with the cooked vegetables. Add the quinoa and pepper and toss to combine. Taste and adjust the seasonings, if needed. Stuff each poblano with about ¼ cup of the filling. Warm the stuffed poblanos briefly in the oven before serving.
Tip: Wear gloves when handling the peppers and don’t touch your eyes or mouth with your hands after working with them.