I think the hourly salary mentioned in the video is a bit too extreme, plus it's not actually mentioned in the article. It just seems unrealistically small a payment to exist in Japan's high economical standard. So, let's try to interpret it from another perspective.
It might be worth considering that Japan is a very socially developed country, that is, much of people's income (I guess more than in the USA) generally goes for taxes, so perhaps it's normal for the net of any salary to be a relatively small fraction of the gross. Which of course would apply for any job, not only animators.
There's also that the Japanese are quite reserved toward foreigners, so there might have been some form of discrimination that has reflected in Henry's case. As a gai-jin and a novice in the company, he'd probably been assigned to a relatively low level department - with much work and relatively low pay grade.
As far as I know, a typical pipeline of producing a Japanese animation is to make the keyframes in Japan - done by the respective studio's artists - and then, for economical reasons, do most of the animation in between and the coloring abroad - say in China and Korea (south, of course:)) for example. That'd create strong competition for these particular jobs, so it's logical for these salaries to really be lower in studios, which don't use outsourcing.
As for the overtime, I can only agree. Japanese are real workaholics in comparison to the rest of the world and there are many examples of people there spending days, working and sleeping in their companies without coming home. This however is again a general situation for any job, not just in the animation industry.
So, these are just a couple of assumptions, but personally, I think and I hope, that the points made in the video and the article are at least a bit exaggerated to provoke sensation and attention from audience.
So cheers and let's hope for the best from the industry and for people living up to their dreams