I have encountered this many times when doing test flights in new worlds to check how both RC-included structures and custom structures generate.
For completely unknown reasons, some structures love to sometimes just spawn WAY above ground (Like about Y: 180 or even more) or below sealevel in oceans, leaving very ugly landscapes.
Both RC included structures and custom ones downloaded on the official repository just can't spawn properly sometimes. This happens especially often on medium or big sized structures and structures that are supposed to spawn in water.
My solution would be adding a new config option to let us set a minimum and maximum spawn heights for each structure seperately and a fixed height for structures that generate in water.
The min & max height should work in way so that the lowest part the structure never spawns higher than the max height.