Yes, all of you are correct.
My 2 primary concerns are 1) how "residence" is determined (in the case of an accident claim); and, 2) insurance coverage depending on which credit card I use.

Obviously, if I purchase my rental through the US site, book with an American credit card and show my California license (as I always have), the agency is not going question anything. I could even waive all supplementary coverage (as I also always have), and take my chances with the 3rd party liability (as I assume many people do). As for the legality of "California residence", I do have a California license with an active residence. So, even though I am "technically" not living there right now, I can't see how that would be an issue; particularly as payment on my American credit cards is made through my American bank account and I have a good credit rating. There must be many expats in similar situations.

Claiming the Japanese residency (which is ironically more accurate than claiming California residency for me at this time) might be more difficult in terms of using the California license, which I see as the big obstacle here. I won't go into the details as to why I don't have a Japanese license as that is a really complicated story best left to another thread.

Needless to say, my situation, while perhaps not unique in these global times, is certainly not common enough for rental agencies to build in special packages, I guess.