In a mixing bowl, combine the warm water, instant yeast, and honey. Stir gently and let it sit for about 5-10 minutes until it becomes frothy, indicating that the yeast is active.
In a separate bowl, whisk together the flour and salt to evenly distribute the salt.
Add the frothy yeast mixture to the flour mixture. Stir until a shaggy dough forms.
On a lightly floured surface, knead the dough for about 5-7 minutes until smooth and elastic. Alternatively, use a stand mixer fitted with a dough hook.
Place the dough in a greased bowl, cover with a kitchen towel, and let it rise in a warm place for about 1-2 hours, or until it doubles in size.
Preheat oven to 425°F (220°C). Drizzle 2 tablespoons of olive oil on a baking sheet, spreading to cover the surface.
Punch down the risen dough and transfer to the oiled baking sheet. Gently stretch it to fit the baking sheet. Let rest if it resists stretching.
Melt 1 tablespoon butter and mix with minced garlic, thyme, rosemary, and pepper. Brush this mixture evenly over the dough surface.
Cover dough with a kitchen towel and let it rise again for 20-30 minutes until puffy.
Use your fingers to create dimples all over the dough surface. Drizzle with remaining olive oil and sprinkle with flaky sea salt if desired.
Bake in the preheated oven for 20-25 minutes until golden brown. Melt remaining 2 tablespoons butter while baking.
Remove focaccia from oven and brush with melted butter. Let cool slightly before cutting into squares. Serve warm or at room temperature.