I've built a couple of base blueprints for my own use, one which is mostly above ground but has critical components buried underground, and another which is intended to be completely buried as an underground bunker. I've checked "Terrain Removal" in both of these but when spawning them in, I find I still need to dig out the underground areas before they can be accessed. I'm not surer what I'm missing or if I'm misunderstanding the purpose of that checkbox, but it's rather frustrating that the dirt inside the base requires manual removal with a drill.
Those check boxes only apply to POI's that get spawned in by the game, not structures spawned in by players. The terrain clearing and flattening/offset features only work when the terrain is first generated by the game, hence why it only works for POI's spawned during generation. Anything you spawn as a player or an admin will have to be cleared by hand. Perhaps we will see this change in the future but for now this is how it works.
