Currently URIs in RDF output use hard-coded base parts: http://commons.wikimedia.org/wiki/Special:FilePath/ and http://commons.wikimedia.org/data/main/.
It is however possible to configure non-RDF parts of Wikibase to use custom URLs for Geo Shapes/Tabular Data (see geoShapeStorageApiEndpointUrl, geoShapeStorageBaseUrl and relevant tabular-data config settings). This leads to inconsistencies/wrong data in RDF output.
Base URIs for RDF should be configurable as well as non-RDF paths are already customizable.