Afaik, Balance is done by banner-slots.
The game takes the banners out of banner-files. In those files are different banners (21, afaik). Now you got around 8 files. means you have 168 Bannerslots. Not enough bannerslots for every clan to have 3 banners.
Also, you could just merge 3 clans and use the banner for every clan. With your suggestion these three clans would play as one side on the server, but still have their individual clanbanner. That would result in one-sided Battles. Like it already does again, since HRG and Fallen merged under one banner and swarm the Siegeserver like flies do with dead dogs in hot summerdays. Heading against them are only greys... but they suck at siege.
(Luckily for me that I got my own server with no Stupid HRG on it.
- Oh and its mysteriously always playing the gamemode I want to play.)