Hi Hansis
This is currently not possible.
I highly recommend to always select the whole VM to include the Config-Files in the Job.
As you experienced it is quite complicated to restore a VM without them.
One way to only back up the System Disk is to set everything else to independent.
Advantage: you can select the whole VM for backup and only save the disks in persistent mode
Disadvantage: you cannot snapshot anything besides the System-Disk in vCenter
Regarding the automatic selection feature I heard that HP is working in Labs on something.
No info on what exactly or when to expect a new feature of course.