I think the city of Palumpolum is supposed to be somewhat of a reference to Palom and Porom from FF IV. When I first heard the city's name though, those two were the ones that came to my mind. There's also the airship The Palamecia, which was the empire in FF II.
That's all the ones that I came across that weren't listed in the OP. Of course, I haven't quite finished the game, so there could be more.
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