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.
I believe I read your post wrongly... Lion Server sets up it's own DNS server if it can't find one at install time, so adding the internal IP as a DNS server to your client's network preferences should enable you to access the machine by it's FQDN, provided that the DNS service lists the FQDN.
You can access the DNS server via Server Admin.