Slice onion. In a large skillet, heat 1 tablespoon of oil over medium-high. Add onion. Sprinkle with 1/4 teaspoon salt and cook for 8-10 minutes. Add sugar and continue to cook for 5 minutes. Stir in vinegar and cook 1 minute longer; remove from heat. Stir in spinach and cover.
Roll dough out onto pizza pan (or if desired, use paddle and preheated pizza stone.) Spread 1 tablespoon of oil onto dough and let it rest for 10 minutes.
Meanwhile, mince garlic. Melt butter in a small saucepan. Add flour and garlic; cook and stir constantly for 1 minute. Slowly whisk in milk, remaining 1/2 teaspoon salt and pepper; bring to a boil then remove from heat.
Pour white sauce over pizza dough. Add half the cheese, onion mixture, pepperoni and remaining cheese. Bake 8-10 minutes or until cheese is melted and lightly golden.