The existing location that is forcibly added (from what I can see, but prepared to admit I may have misunderstood) into the virtual-host.conf needs to be added before any other locations are added, otherwise from what I can see an additional root location doesn't work.
I have moved the location to be before the addition of any additional directives provided from the GUI and now WP Super Cache rules needed to provide static caching works.
Happy to go into more detail if this is something that others may need, or happy to accept it's a use case that only occurs for me :)