For my VPN clients that need backups, I assign a static address to the VPN endpoint. Then I use this as a ClientNameAlias and also bypass DNS lookups with the NmblookupFindHostCommand.
If your client is NAT'ed behind the gateway, then you'll have to expose it to BackupPC somehow. But whether it's mapped by the VPN or not, you just need to make sure that the appropriate routing is configured.
Regarding disabling the schedule, look at BackupDisable=1.