Really don't think there's any tech issue here. Server-side can handle another zone on the main continent fine, see the scale of EK and Kalimdor (which both include Cata zones AND BfA revamped zones). Client-side only loads simple terrain geometry beyond a certain distance, and that distance is relatively close, so there's not entity stacking or anything. Plus the nature of a static rather than dynamic environment design means that you can just flag the assets up above to not load until the player is above a certain level: The player is only ever going to see the bottom of the flying islands when just on the regular Isles, so all that's being loaded is the simple rock texture and simplified geometry of the bottom of those flying islands.
If the islands were up high enough that the lowest part of their start is about even/just above the peaks of Thaldraszus (like so), then they won't load much from below, and when you're up on them not much of the main zones will be loaded. They have the advantage of facing the opposite direction. Whenever you're below them, you don't need to load any objects or entities above, because they are blocked from view. The same way games save resources by unloading things behind you, or outside a building when you're in one, or inside a building when you're outside one.