It is possible that there just is no server - a list is here: http://ufoai.org/ufo/serverlist.txt (the masterserver url is in the cvar for the masterserver)
I saw an internet server today in addition to my local ufoai-server. It seems to work.
The server cvars should all start with sv_* or g_* if you need a list, type "cvarlist g_" in the game console. But you might have to start a battlescape session to see all the g_* cvars (as they are created by the server game logic module that is only loaded when a map is active)
Never ever trust that mattn guy. He's a strange one. Always double prove
I think I didn't say that I'm totally sure about it. This is something that must be checked.
Hehe.

I'm experimenting only with 0base.pk3, 0ufos.pk3 and 0maps.pk3 for the server, so far there are no issues.
No, but you can override $HOME envvar - or - if you really don't like that (which i could understand), then i can add it to the latest master.
I think that shouldn't be necessary. Just to explain how the ufoai-server package works:
You can start the server with "service ufoai-server start".
On package installation a new user "Debian-ufoai" is created. This user owns /var/games/ufoai-server as $HOME directory for a simple but system-wide server setup.
There is one default configuration file in /etc/default/ufoai-server with whom you can pass default options to the daemon. By default the server uses a new and very basic Debian specific debian_server.cfg which resides in /etc/ufoai-server/server.cfg.
The executable is located at /usr/lib/ufoai-server/ufoded. In the same directory you can find the base directory but it contains only symlinks to the static *.pk3 files in /usr/share/games/ufoai and to our server.cfg in /etc/ufoai-server.
At last there is the ufoai-server wrapper script in /usr/games. I think a new "path_to_home" cvar isn't necessary at the moment. I can see that all logs are written to /var/games/ufoai-server/.ufoai/2.5-dev/base and I can also place mapcycle.txt in this directory and it is recognized by the server.
All in all the package is usable and simply needs some testing and some fine-tuning of the start parameters.