I did not understand what you mean by the expression "CLI completely different to SSH". If you mean the standard set of commands Ubuntu, Redhat, etc. - on the NAS a reduced system due to the limited amount of internal flash disk.
I compiled the latest version of ownCloud 3 years ago. For this reason, I don’t remember why I used SQLite instead of MySQL. But I am sure the reason for this was.
NAS is not a full-fledged server, but only a "home version", so I did not consider the possibility of using OCC. Most functions can be done via the web interface.
PHP built into NAS does not have the full set of modules required for onwCloud to work. For this reason, I specifically compiled for ownCloud PHP addon. It is also used in some other addons.