Fixes T12884. In cases other than this UI, applications access URIs through the Repository they're part of. This means that applications interact with URIs which have gone through the correction/adjustment logic in PhabricatorRepository->attachURIs(), which fixes up "builtin" URIs to have the right values based on configuration.
In this case (and, as far as I can tell, only this case) we load the URI directly and act on its properties which depend on configuration and repository state.
This can mean we're using a different view of the URI than we should be.
To fix this: after loading the URI, reload it through the repository so the relevant adjustments are applied.
I think this is the most reasonable fix. We could try to make RepositoryURIQuery somehow enforce this, but the cost of this error is small (mild confusion about display state), the other things which do direct loads don't depend on this state (editing), and everything else loads via a repository and is likely to continue doing that forever.