I am not sure that the three truly merged. I don't think that too many dojos that were formally USAF-WR stayed in the USAF. Chiba Sensei's students tend to be very loyal to him. The East-West division in the old USAF had somewhat less to do with geography and more to do with which Shihan's lineage a particular dojo came from.
As I stated, there is much more to the story than what I wrote. I am a third party to knowledge here and a novice Aikidoka to boot so it's not my place to say anything more than I did. Those of you who know more about the history of the USAF know why.
When it comes to the spirit of Aikido, I think most of us would agree that the affiliation or style doesn't matter. Call me naive, but although lineage is important to me it wouldn't stop me from training if I didn't have access to an Aikido dojo that had a direct connection to the Hombu dojo.