But the backup is done by the VirtualBox
If you re-install, new instantiation, or upgrade, your config files are in /etc. What you need after the fact, is access to your config files. It makes it a much easier task to copy your working configs, to the new installation, rather than having to re-edit the default files, to make a working installation. Its up to you how you back things up. Just make sure you can access files such as /etc/fstab ( just an example ) from your backup.
FWIW, I usually make a copy of /etc, store it in my /home/user/ directory, upgrade, and I do not format my /home partition. Then the old config files are easily available.
Don't want to make a big deal out of this, but you do have to think ahead.