This is a known issue, and unfortunately, I don't have a good solution for it. Block checks are unreliable because the islands are spawned as structures which by their very nature don't play nicely with block checks. I believe there is a setting in Minecraft Worlds that allows you to specify a minimum distance between BO3's, but no such setting exists in TerrainControl. If a feature like that gets added to Open Terrain Generator, then I might be able to fix it by migrating to it, but until then, this is just the way it is. Sorry about that.
On the bright side, having an island on top of another makes it easy to mine the underside of the upper island, and because ores tend to favor exposed stone, you're likely to find loads of useful blocks that are fairly easy to reach. Mining is usually a real pain in a shattered world, y'know?