Great post and I was thinking about this same issue the other day. I think this is why Uber seems to be playing up the logistics/on-demand delivery route for future growth. Unless they get serious about vertical integration with manufacturers they are not likely to be able to compete on price in the long run.
However, Amazon also sees this opportunity to create logistics as a service and they will likely “rent” out capacity, as they do for AWS, in order to create greater economies of scale (which reduces their own unit cost for warehousing and last mile delivery). So its likley they are going to get squeezed on both fronts and might end up focusing on licensing their software instead of physical transportation.