In a large bowl, combine the flour, 1 teaspoon kosher salt, and instant yeast. Add the water and mix until a shaggy, sticky dough is formed. Cover and let rise until doubled at room temperature for 1 ¾ to 2 hours.
Heat a large sauté pan over medium heat. Add 2 tablespoons olive oil, then the onions and 1 teaspoon kosher salt. Cook until medium brown, about 25 minutes. Scrape onions onto a plate to cool.
Line a 9x13 cake pan with parchment paper and drizzle 2 tablespoons olive oil over it. Scrape the dough onto the oiled parchment. Drizzle the top with another tablespoon of olive oil and dimple the dough. Let rest for 15 minutes.
Preheat the oven to 425°F. After 15 minutes, dimple the dough further if needed. Let rest for another 15 minutes before scattering the top with onions, poppy seeds, and a few pinches of salt.
Bake for 25 minutes until deeply golden brown. Prepare any toppings while it bakes.
Loosen the focaccia and slide it onto a cutting board. Cut into 12 squares and serve immediately.
