That said: is racism a bigger problem in Japan than e.g. in the United States? Oh, yes. Unquestionably.
This is totally ridiculous. I lived in Japan for a year and as a white male, it was the first time I experienced being on the receiving end of racism. It sucked, but was a good lesson into how it feels.
Not sure which London you've been living in (or visiting) but I would say there are many more choices than the three you outline above. I know many people here who work in startups/online media/web dev etc.
The one thing I will agree with is that it's not cheap. I think it is fair to say London is probably 3X more expensive than Berlin.