I think the territories a faction controls are enough 'big stuff' to prove how influential a faction is. I think every faction should get an equal size plot, something in the neighborhood of 25x25x50. The 5 floors would be symbolic of the 4th, 3rd, 2nd, 1st and Founder clearance levels. Not much else. As to location within the city, first come first serve. Special rules requiring specific locations for how the offices are arranged could be handled by the server admins. Someone might move their offices to a 'better' location by diplomacy or earn it by beating w/e faction occupies that slot. Again, this is all managed by the server.
As to who builds it (plus when and where) I've rebuilt Deathmark city twice. Once from a procedural city and again from scratch. So I can provide some idea of what it might look like. But I'm not in too big a hurry to re-re-rebuild. Here's what I had laid out (along with some old features) before I scrapped it:
-Main office (Admin controlled, had build block inside)
-main office garden (trees, 'fountain' looking thing, respawn point, a freebie box)
-outdoor player shops (like on of those arts n crafts shows with little areas for each shop, intended for a shop NPC to be placed)
-large store (NPC trader controlled, ten story thing that just really housed the shop block)
-factory (several areas for different factories, all 'permissioned' to allow newbies some speedy processing)
-power plant (just a big ugly thing filled with reactors)
-bar (just for fun, built underground)
-space elevator and docking platform
-unfinished space port
-unfinished 'natural' park
-planned: small homes (temp for newbies, long term 'rented' for loners)
-planned: museum/art gallery
-planned: skid-vehicles with free access
-rented storage (for those lone wolf types)
-other decorative features with a few hidden surprises
-unfinished tourist info booth
The original city could be used as a tank arena as well. Pholo, a few others and I had tested its playability and it was ok. People would steal the tanks and cars but it didn't matter. That'd be harder to do now and the new rail system could offer a fun mass transit solution any how.