I haven't spent ten years in Japan, but I have spent some time there. Some of his complaints do ring true especially around civil rights, however his experience of it feels very weird. I was praised for my language skills, accepted and invited to family outings, never had issues with restaurants that had no foreigner signs (after I spoke Japanese even badly it was all fine so long as acted within their cultures manners) and the police were nothing but helpful, gave directions etc, outside of Tokyo they even gave me a ride when I miscalculated a hike.
So yes I agree Japan has huge issues... however I can't really explain the toxicity of his experience.
Yes I'm white non Asian, pretty tall, and pretty certain they won't ever mistake me for a local.
They also always used the San or other appropriate honorifics, it helps if you adopt a 'japanified' name and introduce your self that way.