The prefixes Wikibase uses for Turtle and RDF/XML output are hardcoded in the RdfVocabulary class. It would be nice if they were configurable. The prefixes have no formal meaning and the output is valid as long as these prefixes are mapped to the correct base URI, but it'S still very confusing for 3rd party installs to use the "wd" prefix.
If this becomes configurable in Wikibase, it will also need to become configurable in the query service.