As MailInABox is not trying to protect the server from physical access, it doesn’t concern me that the files still can be accessed when someone has root access.
It could be that when upgrading to newer versions, some things break:
The encryption backend has changed in ownCloud 8.1, so you must take some additional steps to migrate encryption correctly. If you do not follow these steps you may not be able to access your files.
I ran @JoshData’s script to unlock the OwnCloud admin account and the only two changes I made were enable file encryption in owncloud & I turned off “Federated Cloud Sharing” because server-to-server sharing seems creepy to me & I didn’t want people randomly doing that — I hope it doesn’t break anything. If it does I’ll revert to fresh install and honor Josh’s don’t touch anything in there.