I was in no way defending that system at all. I was just pointing out that the 99% statistic is constantly thrown about in Ghosn discussions without ever mentioning what the conviction percentage is anywhere else. And if you use the US as a a standard of comparison then that statistic is actually quite high as well. And if use the same calculation as Japan then the US is also above 99%.
If someone says "the life expectancy for women in my country is 88", then without comparing that to somewhere else perhaps your own country then you don't really know if you should consider 88 high or low or normal. Anyway the link I provided discusses comparative justice systems and why this is, including your first point.