heya twig
by default all bases have an increased height of 1, and they will spawn normally unless they were not copied properly. you can use autoheight, but the base really should be recopied when it spawns underground or too far into the water
when copying a base, stand in the center, on the foundation, while looking at the foundation. verify with /paste before using it again. the top of the foundation should be near slightly above ground by about 0.2 to 1 meter (ideally 1.5 but that's difficult). the increased height of 1 will be sufficient to keep the majority of the base above ground. small sections of the base going into terrain is acceptable, and any boxes clipped under the terrain will be destroyed (by default) and have its loot moved into other boxes.