Conversely, sometimes "thing you don't like" still has a redeeming quaility or two.
Sure. Doesn't really change my point about nuance.
Can we look at this works, at certain ideas of his in isolation, or, interestingly, in conjunction with his character defects?
Again, sure, but I'm also going to ask people if they considered the things they borrow or just lifted them without thought. If you say, "I combed over this theme or idea, and I really think I've pulled from it in a respectful way that leaves behind any harmful message" then I'm certainly going to be happy with that discussion.
The issue for me is a lot of stuff (not just gaming) lifts from shit without a care in the world, which is how you get redemption arcs for people that look like Nazis:
Birds aren't racist or problematic. Numbers aren't, nor are skulls, or the color black, or certain poses for birds, etc.... But in aggregate, I think this was a pretty poor move by the author for what he intended for these characters. "Wouldn't it be neat if they looked like Nazis" is an idea that wasn't given care at all, at least as evidenced by the work itself.
Creative works are always open to critique. That's the point. And my critique of works that sample from harmful shit is "I wonder if they know or care about the history of these things" usually followed by the disappointing conclusion that "No, they never had to consider other perspectives at all." In the above example, I find it unlikely that the author (Oda, a lifelong Japanese guy, which isn't a country with a lot of people in it affected by the Nazi campaign specifically) ever thought about how people would react to that imagery. He thought it looked cool, drew it, and then moved on. That's certainly his right; creatives can make what they want. But it's my right to say that's harmful, that it was a bad idea, and that ultimately the work would've been much better if he had done something else or had properly given these choices some thought.