I believe the developers have said Novigrad is based on Amsterdam, even though it has cognate names with Veliky Novgorod and Novigrad of Istria.
The Nilfgaardian Empire can be equated with any of several real-world empires, including the Western Roman Empire, the Byzantine Empire, and Nazi Germany. I find the Holy Roman Empire less persuasive, as the Nilfgaard Wars don't equate well to the Northern Crusades. The actions of the Flaming Rose are to me a better match for the Teutonic Knights and the Northern Crusades.
The Nilfgaardian claim that the invasion is to bring the benefits of advanced culture to the North is as hollow as the ancient claims of the Romans. The undisguised purpose of all imperial expansion, including that of Nilfgaard, is to acquire valuable land and settle it with loyal nobles, while displacing, subjugating, or exterminating the indigenous people as necessary to this end.
There is no moral high ground to be had in this conflict. None.