Preheat oven to 400 degrees F. Coat the inside of a 5-1/2 quart Dutch oven (or oven safe pot) with vegetable oil spray. Add sliced onions, butter, and salt. Bake for 1 hour, covered.
Remove from oven and stir onions, making sure to scrape up any onions that have stuck to the sides of the pot. Return to oven with the lid slightly ajar. Continue to bake for another 90 minutes until onions are light brown in color and onions have dramatically reduced in volume. About 45 minutes into cooking, stir onions to prevent any burning along the sides of the pot.
Remove from oven and remove lid. Place on stove over medium-high heat. Stirring often, cook for 10-12 minutes until onion liquids have evaporated and onions are golden brown in color. Remove from heat and allow to cook while you prepare pizza dough.
Increase oven temperature to 450 degrees F. If using store bought pizza dough, allow to come to room temperature. Divide dough into four equal parts.
Spread about 1/2 Tbsp of olive oil in each mini cast iron pan. Place pizza dough in oiled skillet and gently push and pull dough to fit skillet.
Combine 2 Tbsp olive oil with dried thyme. Spread about 2 tsp of oil mixture onto each dough. Sprinkle about 1/2 cup of caramelized onions over dough. Top with about 3 Tbsp of shredded gruyere. Season with black pepper.
Transfer skillet to stove over medium-high heat. Warm up the cast iron skillet and cook pizza for about 2-3 minutes until the bottom of the crust is set and the oil is bubbling around the outer rim of pizza. Transfer hot skillet into preheated oven. Bake for 10-12 minutes until cheese has melted and is golden brown in color.
Remove from oven and let pizza sit for 2-4 minutes before unmolding and slicing.