When configuring a reference repository in the Git SCM (configuration of the Additional Behavior > Advanced Clone Options), the console output does not show anything about the fact that it is using a reference repository. So it is hard to confirm whether the configuration is applied and operational. However any error would be logged correctly - referring to the code
It would be great if there was a line telling that the clone points to a reference repository.
Note: We can check that when the repository is cloned in a workspace, the .git directory has a file objects/info/alternates which contains the location of the reference repository (under $JENKINS_HOME/workspace/<jobName>/.git).