I haven't played with this tool, does it update the terrain real-time? Cause it was possible to change terrain in Civ5 (like removing a mountain or making coast into land or land into coast), as proven by the InGameEditor mod, however the graphic engine would not update the map in real-time, so your new land would still look like coast until you quit and reload the game. Not very convenient.
As for the Engineer himself, i would rather have a canal improvement allowing boats to move between bodies of water than actually turning an entire tile into water.