Server 2008 R2 Hyper-V backup options

I am in the middle of configuring Networker 9 with professional services and there is, apparently, an issue with the client and Server 2008 R2 where the HyperV guests cannot be backed up through the host. The engineers have installed agents on all VM's and have backups running on the guests as opposed to backup of the HyperV server's file system and the vhd's. I would think that recovery is much quicker if there is just a vhd and config file to restore, as opposed to what would be, in my mind, a bare metal restore. Am I off base here? If anyone can present the pros and cons for me, I would appreciate it greatly.