So sometimes when I lift props in the air to work on under them then it says they are out of the room. My suggestion is the room boundaries extend to be invisible around the building all the way to the ceiling. I don't know if this is doable but I thought it should be this way in case you lift your boat up to make one last tweak and then it disappears.
I'm not sure about it but I think this is to keep players from building boats the size of skyscrapers. Someone who disagrees with this might say that that the players cannot go above that spot during the build phase, but they can during the water phase, and it doesn't stop them from making some form of ladder or staircase up to the top. Anyway, I get where you're coming from, and with the current information I have (not much) I agree that perhaps the room thing should extend upward some to help with this problem.
If the boundaries were extended outside of the room then people's props would get removed for even going OVER your room. Not a good feature and serves no purpose, not going to back this idea.
You stated "all the way to the ceiling" this means that the boundary where props would get removed would also be "all the way to the ceiling" meaning they can't move boats over your room if needed.