The target market won't know how to keep their system up to date and won't know how to use the shell
ownCloud comes with an updater app, but it only covers ownCloud
An intermediate user might be able to find documentation on how to use the OS' package manager, but will probably overwrite key files
Default, recognized repositories have to be used
Path to a solution
Ideally, there should be an app within ownCloud, capable of updating the OS. That's how the NAS providers do it (apart from the fact that they ship a big patch instead of upgrading each individual apps)
Key config files need to be blacklisted. The default behaviour during an upgrade will be to keep existing config files (until things fail, unless we can be proactive and offer patched version of those files)
Snappy core is kept automatically up to date and users have the choice of either using an ownCloud snap which contains ownCloud updates or one which lets them use the ownCloud updater
Situation
Path to a solution