I understand that this pertains to RPGs and not necessarily war games, which are my forté, but something you should know regarding the last point - and this may apply to some of the others as well - is that anything set in WWII is going to have this problem. For example, I'm Russian, and despite that fact that I hate communism - with a passion - were I to put myself in such a setting, it's not about the ideological struggle between two tyrannical systems, both of which I thoroughly despise, but the existential threat to my entire country ("country" in this context having nothing to do with the "State"). BTW, the Americans weren't the "good guys" either, but that's a rant for another time.
Not to seem rude, but considering the potential implications, then perhaps historical settings might not be for you at all. History, after all, is a never-ending series of atrocities that have all been concealed and/or justified in their own day while also, in later days, being exaggerated for ease of vilification. The Middle Ages, for example, were certainly unpleasant times, but not quite as bad as people typically believe, thanks to some quasi-propagandistic misconceptions dreamt up during later eras, mostly the Victorian period; Ius Prima Noctis, for instance, was not a real thing.
RE: What are your roleplaying scenario red flags?