If the city covers the whole planet, where do they grow food? Why isn't staples like flour, eggs, milk etc in high demand? Why only luxury food that perishes? Why does it perish? they not heard of packaging? If we can transport fruit around the world, in big slow ships, by filling the hold with nitrogen, how come we forgot to do this after we fled the coalition?
luxury food:
Well, at this moment we use cheminical agent or simply, cold, in order to slow down the food spoiling reaction. It is easily possible that luxury food - which, if I understand, is made of native alien lifeforms, doesnt go well with any of the known cheminical we use, nor cold.
Also; if the city covers the entire planet. Well, I somewhat doubt that, but I believe the entire planet would be -covered-. If planets were entirely covered, we'd have Coruscant, which is by far, the most extreme case of a city planet - but even there, according to the books, there were mountains to ski on (yes, I love those cute details in sci-fi book.)
So, I guess a planet like manhattan would be partially city, partially industrial plants, partially agricultural, depending on regions.