I think I have in essence what you are asking. I do have the ability to access a website I host on my Lion Server through a fully qualified domain name (FQDN). Typing the url into my browser pulls up the website without problems. I have also cleared browser cache and reloaded pages w/o issue. I use dyndns for dynamically updated external ip address.
I also have VPN services working w/o issue from my iMac.
But when I try to access it via Server app I get the log in dialog and when I select the listed server that I want to access (it's listed name is my FQDN with local ip address) and fill in my password it shakes like I have the wrong log in info.
If I use the Server App and enter the local ip address it connnects with the same user name and password that I used before.
Note my server and the computer I am using to administer it are on the same internal network and I'm trying to get this to work so I can install the Server App on my macbook which I will use to adminsiter the server when I am away from my home network.
I have also tried to connect via the VPN without success when using the FQDN.
I don't know what the specific port is for Server App.