Until InitLevel is not COMPLETED, unknown/anonymous user is used for tracking changes in configuration files as is defined at
https://github.com/jenkinsci/jobConfigHistory-plugin/blob/master/src/main/java/hudson/plugins/jobConfigHistory/JobConfigHistorySaveableListener.java#L88-L93
SYSTEM user looks like a better option (as the changes are done by the system at that point).
Done in release 2.22.