Don't know if there was a mistake earlier, but the water seems to render underwater after all, no matter how small the area covered by the marker is. The biggest problem was rendering the surface anyway. I solved that by breaking the rooms apart, adding a new room marker on the surface, covering a large area (and the pivot point) of the water surface and joining the "surface rooms" using it. I have shallow areas after that, so I could just use multiple water objects. The joined rooms seem to render separately anyway, thanks to walls.
Seems like the water object is rendered now always, overruling any room markers and occlusion objects.