Originally posted by: AssertnFailure
Here's the inconistency, however...
Unless the city was built in a hardcore-defined valley or something, then most of the city being below the cloud surface would imply that most of the island surface would be below the cloud surface as well, however that doesn't seem to be the case.
It does seem inconsistent, but there could be explanations. For example, perhaps the island isn't completely level or that it was pushed up to varying elevations like anphorus speculates. Or, since the growth of Jaya after being boosted into the sky is highly unnatural - the animals and trees are huge - the surroundings could've have "grown up" beyond where the city lay. The city, which is made of nonliving material, seems to have retained its original size.

All in all I don't think it is important to logically place the details. The episode shows Robin digging downward into cloud so that means that the city is simply there beneath the clouds at that spot. It seems to have been done it this way to present a hidden, glorified city for Robin to discover to lend more significance to the natives' struggle.