I also work in Japan, and I've always been treated politely. Of course, there's the occasional politician who announces that all crime in Tokyo is committed by foreigners, but real people tend to be a lot more level-headed.
I wouldn't read too much into it. I'm white (living in Austria) and I also get a lot of questions like that from people I just met (although it's normally "do you want to go back home?" rather than "when are you going home?").
I think that in countries for which immigration is a relatively new phenomenon (unlike the US/Canada/Australia/etc) people are in some unconscious way more reluctant to believe that it's actually possible for people to move to another country.
EDIT: how do I quote?
Not a few of those who asked me that question (or the version you quoted) have lived in other countries and are otherwise open minded. Still, probably subconsciously, they see someone (even if s/he's white) as some kind of different person. Yes, US/CAN/AUS are different and that's why their birthrate is sinking but it will not get negative in the coming decades.
It doesn't mean "go home!", it's much subtler. But it surely does NOT show "interested in you, your life and your background".
> Germans probably don't expect that other people like it there.
(Danke für die Vorlage) If you live abroad a quick test for you: Imagine, in the country where you live, you get asked the same question(s)? How would you feel? And then (on the top of that) one of the natives even says we "don't expect that you like it here". Quite subtle...