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I see thousands of Geocities URLs in some directories; so not quite true.
Take the ODP for example. They do not equate one domain with one website, nor do they equate one website with one domain.
A domain such as Geocities could quite easily have thousands of listable websites.
Someone else, with multiple pages in multiple folders spread across multiple subdomains on many different domains could very easily have the entire collection of content tagged as all being part of the same one website, especially if it is all from one related business, or set of related businesses.
Directories try not to do "product listings" so will not be interested in listing multiple pages, or folders, or subdomains, or domains. They want to list the one root domain that the surfer can start at to locate all of the content that you provide, however, or wherever, you have chosen to widely spread it out.