If I look at an American map of Europe, a German map of Europe, and a French map of Europe, they'll all have different names in various places. Now an empire that imposed its will on a region might give its own names to all the cities in the empire. Maybe the locals don't use the imperial names, but an imperial map would. That would explain the common naming system across different cultures. So I don't think the names are much of an issue, if they're meant to represent names used by the mapping culture rather than the local name.