Under Junon is never referred to by anyone in the game and is only seen in the menu, so in the English version it could easily be seen as not the place's name but just "the place beneath Junon". It's clear in the Japanese version that it is its name though, because it uses katakana for "Under". The Turks novel removes all doubt that it is the town's name in English. Maybe the town was originally called Junon, or maybe the town had a name but everyone forgot after they built Junon ten years ago or whatever. :3
The south side with the airport is called "Upper Junon" (and is also called "Aljunon" on one screen), and the north side with the harbour is called Lower Junon. But both sides are multi-layered. You can see this easily by running from one side to the other. Up the elevators by Junon Branch you can see the text "SRJ-L" and "SRJ-R" on the walls for the two sides.
Edit: For bonus confusion, BradyGames uses all the names in all the wrong places. Junon Harbor is not used to refer to the harbour but to "Under Junon", "Lower Junon" is used to refer to both Lower and Upper Junon, and "Upper Junon" is used for Junon Branch. Even Versus manages to fuck it up despite being mostly written from the Japanese game, calling Under Junon "Lower Junon", and both sides of Junon as "Upper Junon" and "Al-Junon" (although distinguishes with "(East Side)" [upper] and "(West Side)" [lower])