Pretty sure at this point that the Multi-faction dilemma has begun to warrant its own thread. Personally, I endorse multi-faction character's within reason.
Take my character for instance, I'm part of the One Sith, but I'm part of the one sith for training and connection purposes. However, my primary faction is the Primeval, so most of my support of dominions and development and such goes towards the Primeval. I wouldn't consider myself as any ally in either dominion because I have a legitimate reason for being in either instance.
If it make sense story wise, and it develops connections with other factions, I don't see why it shouldn't be that way.
Also, I feel like this whole business on allies exceeding faction writers seems a bit far fetched to me. It seems to be pre-emptive to a problem that doesn't exist... I have yet to see a single dominion (to my knowledge, Fringe might of done something) where the non-factions out weighed the faction members. Even if it was that, perhaps there is a perfectly logical reason as to why that is. If I'm not mistaken, as memory is coming back to me, I'm almost certain that the Fringe used a public Auction as form of dominion by taking over the planet's economy over night through the revenue or something to that extent. Seems fairly reasonable to me if it makes sense, so why bother filling up the rules page?