This may be a bit unpopular but I sometimes wonder exactly what Hombu adds to the equation. Sure, they give the yudansha an Aikikai stamp of approval but beyond that I'm not sure they add much. Maybe they do/did a lot of work behind the scenes which I don't see? Maybe I'm thinking of them as a trade organization and they don't see it that way. Please correct me if I'm wrong in this perspective.
PS: I was part of an independent dojo in my formative years and we were very open to all styles and arts. Certainly more open than most. It's not the structure that makes the community work but the people within it.