The default approach for the transformation is to create properties under the given agency's namespace so that it can be linked to or extended easily. If SDMX agencyID is detected, the property descriptions point at SDMX-RDF URIs.
Some publishers would prefer to use the SDMX-RDF URIs directly instead of creating new properties when the agencyID for the code lists or concept schemes is set to SDMX.
So, this should be possible and configurable with a simple switch.