Just two observations I can add. In image #2 of your first post, I think that is by design now, or at least a side-effect, as I have noticed in my own game stairs will cut a fence that is at their top, meaning I no longer have to create my own gap in an open stairwell fence. Not tried it with wall or foundation myself, though I think I will try it just to see. The bit about the terrain raising makes me suspect something is trying to pull the basement higher as you work on your build (almost certainly not by design). Terrain will always cover the basement.
Later: With the ceiling on the basement, I get "incompatible with terrain restraint terrain tile" when trying to place stairs partly under a foundation whereas with the ceiling removed the stairs place but cause odd indentations in the exterior foundation.
