A serious guess is that sky island clouds are either more dense and less buoyant than other clouds, or the fact that there is a sky island sitting on them brings them down below the level of rainclouds
Or they could have just been lower to begin with. They’re white and fluffy, so probably magical cumulus clouds, and cumulus clouds sit lower than rainclouds
I made a like a 200 hundred essay on how everyone in Skyhall should be dead before editing but I realize that it looks too good and I just like having fun in video games without nitpicking