For an easier implementation and due to the need of loadbalancing, i'd recommend not to run multiple instances of maps being played at the same time on one server / one tremulous process.
If you are going for a galactic conquest mod, i would say that each moded server plays one and _the same_ map over and over again. With your "depending on who owns this map/planet"-changes as you like em.
The more servers you got, the more planets are there to conquer. You get a kind of dynamic "universe" with a lot of players online and have a poor-mans clustering all the same.
And I don't think you would need a server-register other than the existing one for that. The moded client can group servers together by their group- or "universe"-name.
I'd ask you guys to think simple and in small steps. There is much brainstorming here but little solid.
As some extra point i would suggest not to mix this discussion with tremulous base development. Lets get a stable 1.2 first an then we will see.
happy tremulousing, i hope you got some piety for me, beeing offline at home so i cant play :-/
greets
Mana