In my experience, it's less gaps and more lack of mainstream brands. The example that comes to mind is ketchup. At Whole Foods I can get generic store brand ketchup or a variety of fancy ketchups that cost 3-10x as much, but they don't have any variety of basic Heinz on the shelf. This "mid-market" gap is common for virtually every product category.

That’s true, but intentional because of the focus on organic and avoiding certain ingredients. That is one of the reasons why Whole Foods is better.