The problem is that the Surface Layer uses texture coordinates (or computed terrain coordinates) rather than "final" displaced coordinates, so that it can match displacement and colour. If you use the Distribution Shader V4 instead you'll find an option to change the altitude key between "Final position" and "Position in texture/terrain". This is a relatively new option (previously it was only possible to change the slope key, and only in the Surface Layer). I don't remember the exact reason why I didn't add this to the Surface Layer yet (there was a reason...), but I will probably do so for the next release.
Over a larger area "Position in texture/terrain" will give approximately the right results. It depends on how large the patch size is in Compute Terrain. For now, if you can use the Distribution Shader V4 that should allow you to make it work.
Matt