The point of the lawsuit and detailed in the analysis is that ALL online purchases end up being influenced (controlled?) as a result. This creates prices that are 30-45% higher across all retailers for a given item.
That would include Amazon Prime subscribers and random internet guy buying the same thing from a different site.
If Amazon controls their own storefronts, that's one thing. When they can exert control over competitors' storefronts - or worse, all competitors' storefronts - that's a different matter.