A lot of these stories are about a quest to discover what is truly right or good. You never just have something be good throughout. It just kinda emerges after enough adversity and the spilling of enough blood to shock people into a revelation.
This goes back centuries too, Musashi is known for basically dishonorably fleeing a duel with Kojirou and hitting him with an oar and a bunch of other random dishonorable things and he's one of the most beloved figures when one thinks of samurai. It's always a lot more gray than reactionaries want to believe.
Yeah well that's the difference between Hollywood history and real history. It's never historically accurate, even when they claim they are "based on a true story", and the people involved are STILL ALIVE and could be contacted to fact check things. They will still take "creative license" with facts, because story. So I don't really care that something that is obviously fiction, isn't accurate in itself, I assume none of it's true, and just enjoy it as a story.
I am bothered however, by how many people take the details as portrayed in fiction, as fact, and color their worldview as a result of that. THAT part, is where I think the "smudging of historical facts" is problematic. But if the creator makes a point to not say "THIS GOOD, THAT BAD" very definitively, and it's presented as debatable and/or questionable, I'm fine with it to an extent.
So on one hand, I don't have an issue with a culture, that has a less than pleasant opinion on historical japan, being annoyed at their presentation in something. But on the other, I'm like "Yeah well it's fucking fiction, just like the majority of the korean movies/shows that positively portray your culture during that same period."
It's all a mess, yay history and people's devotion to it! I swear I wish people would stop giving so much of a shit about history, especially the further back it goes. It invariably has less and less direct relation to current life, and is prone to historical/heroic revisioning, in a way that just serves to isolate and divide us.
Yeah, back in the 13th century, it's good odds that EVERYONE was some flavor of Weapons Grade Deuchebag, but they're all dead, so don't construct your life based on how they lived theirs.
*rant mode off*