I've never seen any screenshots of SH3Gen maps containing any 3d terrain. Neither can I remember that Global Explorer promised such a feature. You don't even need it. There's not much terrain in the sea to walk onto you know. So, not really sure what you are looking for. It does what it is supposed to do: make 2D maps with SH3 intel.
With the latest free TatukGIS viewer. (image resized 50%)