This would allow greater compatibility with CubicChunks, Terra++ and other mods that alter, expand or remove the normal Vanilla height restrictions. These mods often define Y=0 as sea level, and allow Y to be negative. Since the sea is below sea level, this means that ocean biome fish pokemon currently can't spawn in CubicChunk oceans at all (tested).
Additionally, the current spawn rules seem to have 'seafloor ' pokemon spawning on the coast, where biome = Ocean and Y > 0 (apparently there is no check to see if their spawn block has water above it). This feels minor compared to the empty oceans however.
River spawns are less affected since rivers are typically above sea level.