Although I disagree with the proposal, I do agree with the one that gives Utopian players a random nationality.
I totally agree with what you are saying in terms of "in this game, Utopia is a country, with players with that nationality, so why wouldn't it have an NT". It doesn't make a lot of sense, but your change would create a lot of problems... from "NT of Superteams" to where it should play.
That's why I think giving players a random nationality is the safe way to fix what you think is wrong.