I spent way too much time on this and thought others could benefit from this also. I wanted to install OwnCloud 7 using MySQL. I am syncing my computer using BTSync and wanted to be able to share and browse files using Owncloud.
During the process of figuring everything out, I feel like I kept fighting with OMV. In its attempt to lock everything down and control the config of the server makes this sort of thing far too clumsy and difficult. I really like the idea of OMV, and don't really want to learn about manually managing RAID, spin down of drivers, health checks, etc. That's why I'm sticking with OMV. Otherwise going straight Ubuntu and using something like Saltstack to configure everything would be the ticket. With a tool like Saltstack, the server configuration can be checked into source code repository (like Github). Configuration can be versioned and easily repeatable without a bunch of click configurations.
I ended up installing MySQL and owncloud outside the OMV plugin system. I struggled a bit with NGINX configuration, so ended up using the configuration file from the owncloud plugin. Here are the instructions: