Part of this is overregulation, with zoning and planning departments enacting policies that make smaller retail spaces less attractive to builders and owners, leading to a low supply, and allowing egregious rent for well located small retail.
Yes, economies of scale likely mean that larger businesses can afford lower prices, but smaller businesses also get to avoid some costs (no large administrative corporate departments necessary for a one-location bodega), so the prices probably don't need to be as far apart as they are.
Robinson-Patman is terrible law that’s more or less impossible to enforce equitably. So it hasn’t been.