Gently stir yeast and honey into the water and let sit for 10-15 minutes. In a large bowl, whisk together flour, thyme and salt. Let sit for 10 minutes.
Add yeast mixture to the bowl together with the olive oil and mix. You want the dough to be sticky, so don’t add too much flour.
Transfer dough to a well-oiled 9x13-inch baking pan. With oiled hands, gently stretch the dough across the surface of the pan so it is evenly distributed. Drizzle olive oil across the top of your dough. Add toppings, cover and let rise somewhere warm for at least 1 hour.
Bake at 425°F (220ºC) for 20-25 minutes until golden. Optional: to get the cheese a little crisper, place under the broiler for an additional 2-3 minutes keeping a close eye. Let cool for a few minutes, then loosen from the pan and transfer to a wire cooling rack. Finish with flaky salt and fresh thyme leaves prior to serving.