Reconstruction constraints for water - Override the 3D construction

The reconstruction constraints for water appear a bit useless. According to the help file it only fills in holes in the model. Usually I'm not concerned about areas missing data over water, but more concerned with the large lumps that are constructed in the water surface.

In my example below I have added a constraint area from a KML for a mesh of a river and road. The constraint has filled in the area to the right of the model, but has left untouched the mountain of water that is the river.

What is the best way to override the 3D construction of water areas?