The civic centre is arguably the most important structure in game: it has a territory root and a significant territory influence radius, is a dropsite for all resources, provides population, trains workers, and researches phase technologies. Besides, it is the starting structure and the first thing to build in nomad games. Therefore I think it ought to be displayed first.
The order in which entities are displayed depends on the order they're listed in the build and production lists in the templates; there are currently about a dozen structures before the civic centre.
This patch lists the centre, crannog, and colony first, before the house etc.
How it looks in the structure tree:
How it looks in a game sesssion: