If you cut holes in terrain while people are in the server, people won't be able to see the holes. If you save the terrain while the holes are in your server, when people join again, they will get invalid terrain errors.
Also, if you go underground and there is a hole, you won't be able to build, because you will still get a terrain error. It kind of sucks.
As for shape replications, I have no idea. Oh, actually, I do. You could make sure that the setting for place on interior is toggled off. Then you could place invisible interiors wherever you don't want trees to appear. Just make sure they are right on the surface of the ground, and that they z scale is very tiny, otherwise people will have trouble building.
All the gun would need to be able to do is spawn these interiors.