I think alien and native are orthogonal terms. If we landed on an inhabited planet we would call those inhabitants aliens, not to imply that their planet is our native land, but to state that they are different than us. In the same way, the parent comment refers to a nation different from the US as an alien nation.

I don't think "alien" is the most common way to refer to foreign nations, but it's not wrong or rude to my knowledge. Your comment seems uncharitable and insulting though.