Backing up install, tar VS apt-get warning

I am looking to move my Owncloud install to another piece of hardware. The following quote from the manual has left me confused as to how I should procede:

"_When you install your ownCloud server from our Open Build Service) packages (or from distro packages, which we do not recommend) do not backup your ownCloud server files, which are the other files in your owncloud/ directory such as core/, 3rdparty/, apps/, assets/, lib/,and all the rest of the ownCloud files. If you restore these files from backup they may not be in sync with the current package versions, and will fail the code integrity check. This may also cause other errors........"

  • What additional steps are required to recover a distro pkg install from a backup that is now missing "core/, 3rdparty/, apps/, assets/, lib/,and all the rest of the ownCloud files" ?

  • "may not be in sync with the current package versions"? If I am replacing the entire owncloud/ folder, what will not be in sync with what? Arn't all the OC files contained in the owncloud/ folder?

  • As a workaround, can I take the entire production owncloud/ (and it's database), and restore it to /var/www/owncloud_different_name/ on the new server without consequence? The "new server" would be a vanilla Ubuntu with OC installed from packages (but permanently in maintenance mode or something) to pull in deps and whatnot.

On the new system, you use the packet-manager to install the same version as on the previous server (if you want to upgrade ownCloud as well, do it before or after the migration).
Instead of running the installer (the screen on first visit, where you set up the database, data-directory and admin-user), just restore your database and copy the config/config.php and data/-folder into the ownCloud folder.
In case your installer also runs the installation procedure, your restore your database anyway and use your own config and data folder.