The WikibaseClient repoNamespaces setting hasn’t been used in Wikibase since T153769, and it doesn’t really work in a federated world. Its default is also based on the entityNamespaces setting, which means we need to do something about this setting before we can fully remove entityNamespaces (T285472). I think we should just remove it.
Unhappily, while Wikibase no longer uses the setting, it is still used in the Math extension, to build URLs to items. We should probably just change this to use Special:Entitypage, as was done for Wikibase in T153769.