That's a very good point you raise - and one i've been thinking about for a few weeks now: given the source of a lot of/all aikido etiquette, should it all be adopted? Or to what extent should it be adopted?
I mean, as you say: it's from a feudal/hierarchical time - one that is, nowadays, in my part of the world, looked down upon as being wrong/unjust.
I'm not so sure that your use of the term "feudal" is accurate, given that aikido did not originate in a feudal period of Japanese history. Perhaps you were just using colorful language?
As for "hierarchical", contemporary Japanese society is more aware of hierarchy than contemporary American society -- but that's not the sole characteristic of the teacher-student relationship, and I think it's a mistake to try and explain all differences in terms of "hierarchical" thinking.