I think the usage of European history in manga and anime, is because it's both somewhat familiar to the Japanese audience, but also remote enough that it doesn't trigger their nationalistic sensitivities. So writers and show makers can freely explored themes like war, genocide, racism, etc, without getting a backlash or causing controversy in Japan. On the other hand, I think Japanese mangakas like to enrich their worlds with elements from other cultures, to make their works more varied, creative and appealing.