"Exactly, from what little I know of their culture, I think they value courtesy too much to be outright hostile."
They don't even understand what courtesy is.
What they have is a strictly defined system of required phrases (kimarimonku) and actions that serve the purpose of avoiding conflict, but have nothing to do with any actual regard for the other person.
This minuet serves the purpose of containing the murderous rage that lurks just below the surface.
From whence comes this murderous rage?
Very well put. I defer to your firsthand experience and knowledge. I have visited Japan about a dozen times over the last 40 years. It is easy to confuse form for substance.