Im having this same issue on an Ubuntu 16.04 LTS Installation.
I have bonded network I use for my unRAID server which serves my home network and business needs. I have two interfaces I use on the Plex, one for admin purposes and the other is in the Storage Area Network subnet. Plex does everything it should except that I cannot specify the Remote Access IP address it wants to use.
“Preferred network interface” sets the interface advertised to local clients (and a Plex Media Server restart is required for it to take effect). For remote access, Plex Media Server will use the highest priority route (and the interface associated with it). Run ip route from the terminal on your system to see which route has the lowest metric. Based on what you’ve described, it will likely be the one associated with your SAN. If so, you can adjust the routes with ip route delete | add. However, these changes are not permanent. Make sure to stop and restart PMS after making any route changes, and disable/re-enable remote access.