Thank you for your message and your investigation of the Japan 3D Building Data.
With the initial release of this dataset, we clamped the buildings to Cesium World Terrain.
We understand that this may cause floating buildings with the higher resolution terrain data provided by the Geospatial Information Authority of Japan.
We are currently investigating the best way to incorporate the Geospatial Information Authority of Japan data with the Japan 3D Buildings and Cesium World Terrain.
Best,
Dave