It is recommended that both Backup Utilities and an High Availability replica are used as part of a GitHub Enterprise Server deployment but they serve different roles.
The High Availability replica is a fully redundant secondary GitHub Enterprise Server instance, kept in sync with the primary instance via replication of all major datastores. This active/passive cluster configuration is designed to minimize service disruption in the event of hardware failure or major network outage affecting the primary instance. Because some forms of data corruption or loss may be replicated immediately from primary to replica, it is not a replacement for Backup Utilities as part of your disaster recovery plan.
Backup Utilities are a disaster recovery tool. This tool takes date-stamped snapshots of all major datastores. These snapshots are used to restore an instance to a prior state or set up a new instance without having another always-on GitHub Enterprise instance (like the High Availability replica).