Finally found this resolution to the ‘Replica is inconsistent’ error while trying to backup Bare Metal Recovery on System Center Data Protection Manager 2012 R2. Windows Server Backup is required for the server to be protected. The below works for Hyper-V Server 2012 R2 Core as well!
dism /online /enable-feature /featurename:WindowsServerBackup
via System Center 2012: DPM – Replica Inconsistent – Spiceworks.