Just has how Zaunite champions (Dr. Mundo, Singed, and Warwick) can choose to fight for Noxus, Poppy can choose to fight for Demacia. Not to say she doesn't fight for Bandle City as well, her first loyalty is to them. But if there's no conflict of interests, she is willing to fight for Demacia. The fact that one of her abilities is "Paragon of Demacia" indicates this.
Though if people don't like it, they don't have to put in Poppy in with the Demacian city-state champions, just as they don't have to put in Zaunites in with Noxian city-state champions.
From what I can tell, Noxus and Bilgewater don't have a formal alliance. Bilgewater assists Noxians when it benefits them, they'll rob from Noxians when it benefits them.