If I understand this correctly, you are saying that a lake can have a specified altitude, although I haven’t seen how this Is possible. I have tried starting the base altitude level at -1 but the software won’t allow it.
Layer 0 is always the lowest of the 16 available altitude layers. Rather than visualizing a layer as plus or minus a number of layers from a "sea level" (the base layer convention on a geographic map) view it as the lowest possible point on plane before water is added at whatever layer you want the body of water to cover.
If you want to show a region that is two layers below sea level, then you'd set your water level at layer 2 with layer 0 the lowest point on the map. To be accurate in terms of physics, you have to consider "what holds the water back?" when it's set at a layer other than 0, but it can be depicted.
It might help to visualize the "sea level" it terms of a high mountain lake rather than a seashore.