In World machine you can mask most of devices through the specific input node (usually it’s the purple one at the bottom of the device).
You can circumscribe the area of the perlin generator (for instance) using a poly-type layout generator, which limits the extent of the mountains giving them a decent falloff. Then you can create another perlin generator, set it to something smoother like hills and eventually circumscribe them too if needed, and so on until you get an underwater area.
You can use this technique to pretty much compose any type of landscape you want (I once generated a 1:1 map of Isla Nubla, from Jurassic Park).