The reference job provides the builds that can be selected as baseline. If this field is left empty then the same job will be used to select the baseline from. This is helpful if you want to inspect the evolution of issues in the current job (or branch).

If you are building pull requests or topic branches in separate jobs, it makes more sense that the plugin shows the new issues, that have been introduced by a pull request (or branch). In order to show these issues, the reference needs to be set to the Jenkins job that builds the master branch (actually the job that contains a build of the branch point).