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Not sure if this is what OP is getting at but I do believe some of these .io domains are failed projects that are no longer pointing to an active web server.

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These are tld servers, not domains. TLD server are root dns servers, acting as source of truth for the domain names.

No, a root server is shorthand for the authoritative name servers that serve the root zone of the DNS. Here is the list: http://www.iana.org/domains/root/servers

Servers configured to be a source of truth are called "authoritative name servers".

There is no technical distinction between "TLDs" and "domains", they are all just domains, they are just different levels of the DNS hierarchy.

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