Web2Cit works on a per-domain basis. A set of 3 files are defined for each supported domain: templates, tests, and patterns (see Web2Cit Specs).
Given a Target URL, the 3-file set defined for the most-specific subdomain is used. For example, given subdomain.example.com/article, if no set has been defined for subdomain.example.com, the set defined for example.com will be used.
To prevent contributors from defining translation sets for effective top level domains, these should be rejected by the frontend, backend, etc.