There is still some problem with negative values, for some reason the tiles with pure water are getting clipped sometimes. But yes, you could lower the level down to trenches. However, the resolution of ocean data is just 1km, and even though the fractals will make it up down to the ground level, lack of natural features around 100m detail makes it less interesting.
There's also another aspect - the height of the atmospheric layer remains the same, so if you lower the sea level, it also moves the tree and snow line.
So basically it will change the water level dependent on where you are so you can see the lakes and other bodies of water? This will be done automatically I take it?
It needs to be more sophisticated, but basically it will set the level specifically for terrain tiles, and the ones that contain multiple different levels will use an auxiliary mask during the creation. But yes, it will be all automatic.