Heat oil in a large skillet over medium heat. Add onion and cook, stirring often, until softened, about 5 minutes. Add garlic; stir until fragrant, about 1 minute. Add peppers and 1 tsp. kosher salt and cook, stirring often, until peppers are wilted, 5—8 minutes. Add tomato, 1 Tbsp. harissa, and 1 cup water; reduce heat to medium-low and cook, stirring often and adding more water if too dry, until peppers are soft, 15—20 minutes. Season with kosher salt and more harissa, if desired. Keep warm.
Meanwhile, fill a large skillet with water. Add vinegar and ½ tsp. kosher salt; bring to a simmer. Crack each egg into a teacup, then slide each one into the water; reduce heat to low. Poach eggs until whites are set and yolks are gently set, 3—4 minutes.
Divide pepper sauce among four warm bowls and top each with an egg. Season egg with flaky sea salt.
