I have converted a large geoJson into cesium 3d tiles -- wonderful... but not when enabling terrain -- tiles are partially visible obviously due to elevation. Is there something available in FME to consider the terrain?

(assuming the GeoJSON features are flat/2D) You can try and drape the GeoJSON features over the terrain, however, this means you will need access to the terrian in a format which FME can read (e.g., GeoTIFF). It's also likely that there will still be issues where the draping doesn't overlap perfectly but it might give a better result than what you have now.