For the USN journal to work the backed file server have to be added to DPM as Shares or normal catalogs. I have two Files servers added as normal catalogs (each ~500 GB) and the consistency check takes several hours.
According to this
https://blogs.technet.microsoft.com/dpm/2016/02/25/backup-of-enterprise-data-made-easier-with-system-center-data-protection-manager/#comment-10723
it should be up to 60x faster then before UR9
Setup:
2 node Failover Cluster Dell PE430
Storage Matrix MD3820i
Network backbone 2 Cisco WS-C3850-24T
DPM Server is a VM on Windows 2012 R2
Protected Server is a VM on Windows 2008 R2
Every thing is updated