I think the article critically underestimates the typical nth generation student's knowledge of and interest in the Hombu.
It is sort of taken as a given that the further you get away from Hombu the less the typical student knows or cares about the Aikikai. My assumption is that any Aikido school that is in a relationship with the Aikikai is going to have students put on Japanese martial arts clothes, bow and clap, use Japanese vocabulary, etc when training. It seems a little odd that people who would enjoy spending their time doing such things would be so diffident to the idea that there is a five-story dojo in Tokyo that is packed with 7th-9th dans.
There's nothing wrong with the building, I enjoyed the years that I spent training there, but that doesn't mean that I (or the typical Aikido student) therefore wants to support them financially with no particular relationship and no particular return - that's my point.