Note: this relates more to my localized use of Wikibase RDF serialization than to the Wikidata Query Service directly, though it may also be relevant to the WDQS.
It is my opinion that the RDF representation of statement and reference URIs should conform to a W3C standard (RFC5785) so that other libraries (like JSON-LD), for example, can recognize them as Skolem IRIs (or uniquely minted identifiers).
One possible scenario is that a JSON-LD consumer may want to frame an entity, and this would require it to make the statements and references into bnodes so that their values can be formatted as sets or lists. Having these types of URIs in the .well-known namespace simplifies the parsing task.
This seems relatively trivial to do. I have already made the experimental changes in my instance that touches these files: https://phabricator.wikimedia.org/diffusion/EWBA/browse/master/repo/includes/Rdf/RdfVocabulary.php
to produce the intended output attached.