In a large bowl, combine 1¾ cups (420 grams) room temperature water and 2 tablespoons (28 grams) oil. Add flour, kosher salt, and yeast. Stir with a large rubber spatula or wooden spoon until a cohesive dough forms. (Dough will be shaggy and tacky.) Cover and let rise in a warm, draft-free place (75°F/24°C) for 1½ hours, folding dough in bowl every 30 minutes. (To fold, use wet or oiled hands to reach under one side of dough; gently stretch up, and fold over center; repeat on all sides of dough. (See more below))
Line a 13x9-inch baking pan with parchment paper, letting excess extend over sides of pan. Brush 2 tablespoons (28 grams) oil onto parchment.
Turn out dough into prepared pan; using just your fingertips, gently stretch dough to about a 10x8-inch rectangle. (If dough is tight and will not stretch completely, let stand for 5 to 10 minutes and then try again.) Spread harissa onto dough. Starting at one short side, carefully roll up dough into a log. Place dough lengthwise, seam side down, in pan. Let stand for 10 minutes. Using your fingertips, gently stretch dough to fill pan. Cover and let rise in a warm, draft-free place (75°F/24°C) until doubled in size and puffed, 45 minutes to 1 hour.
Preheat oven to 425°F (220°C).
Dimple dough using your fingertips, touching pan through dough without tearing dough. Drizzle with remaining 2 tablespoons (28 grams) oil. Top with onion and cheese; sprinkle with sea salt.
Bake until golden brown and an instant-read thermometer inserted in center registers 190°F (88°C), about 20 minutes. Let cool in pan for 10 minutes. Using excess parchment as handles, remove from pan.
In a small microwave-safe bowl, heat honey, vinegar, and red pepper on high in 10-second intervals, stirring between each, until honey is fluid. Drizzle onto warm focaccia. Serve warm. Store in an airtight container for up to 3 days.