For anyone interested we made some ground on this via Reddit
For those not wanting to visit reddit the short version of the solution is:
What I have done is redeploy the container using the image template and in the unraid edit menu set the path mappings and removed the ports advertised (as this would be handled by the VPN container) then I set the network to none and in extra paramaters I set the VPN container (read more of that here)
Once that deployed I then used unraid update container and it retained the settings. Shout out to u/ErikRedbeard who in the comments above hinted at the retention needing to have the settings set in the unraid edit menu.
In future it would be nice if the portainer settings would be pulled over to unraid as this is a very popular container managment tool.