I'm aware of that, but colonial powers as a whole also tend to have terrible history lessons (as well as some colonies for that matter) which severely downplay the horrors inflicted on first nations, so that's mostly why I believe it was done out of ignorance - your average person is just taught a widly incorrect / softened take on history and never critically analyzes that take because "surely, school wouldn't teach me wrong, would it?".
In particular, from what I can gather online (which I will admit might be wrong) Japanese History classes, much like American classes, have a tendency to gloss over a number of things, such as mostly glossing over Japan's involvement on WW2. And that's a massive, international event with a plethora of outside sources. So expecting that system to tell what truly happened to indigenous people / identity groups outside of the Yamato Japanese is ... not likely.
To make things worse, much like the situation on the West, it seems that there isn't a lot of Ainu representation in general and most of the representation that is there is focused on stereotypes / the past, so I have seen at least one people of Ainu descent say that while the game representation wasn't good it was better than nothing ...
It's just a messy situation altogether :x