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Place oven rack in the lowest position; preheat to 450°F. Coat a large noninsulated baking sheet with cooking spray.
Combine oil, onion and salt in a medium saucepan. Cover and cook over medium-high heat, stirring often, until the onion is softened, 5 to 7 minutes. Reduce heat to medium-low, uncover and cook, stirring occasionally, until very soft and golden, 5 to 8 minutes more.
Meanwhile, roll out dough on a lightly floured surface to the size of the baking sheet. Transfer to the baking sheet. Bake until puffed and lightly crisped on the bottom, 8 to 10 minutes.
Stir oregano and pepper into the onion. Transfer half the onion to a small bowl. Add beans to the remaining onion; cook over medium heat, stirring often, until heated through, 2 to 3 minutes. Transfer the bean mixture to a food processor, add water and vinegar and pulse until a coarse paste forms.
Spread the bean paste over the pizza crust. Top with the reserved onion, tomatoes, cheese and pepitas, if using. Bake on the bottom rack until the crust is crispy and golden and the cheese is melted, 11 to 13 minutes. Slice and serve.