Unless you show me what "Structures", or "Flying Islands" you actually mean, I have no Idea.
I´m currently assume you mean flying bits of Terrain. These can be reduced/tweaked the way I described.
Which in relation to BiomeBundle would mean a lot of work, because you need to tweak every Biome in which they happen.
Edit: Also, I´ve never used BiomeBundle, or even taken a look at it. So I can only guide you to resolve Problems you might have.
Edit: Tweaked the Post