It's really quite simple. Create a separate category for building structures, with different rules, if not already done. Allow them to clip into the terrain, but not crafting or storage structures. S+ has already done this for ARK when used as a mod. Objects can clip, into terrain and other objects, but crafting and storage containers that clip even just a little bit into something else, cannot be accessed. Thus no exploit.
But this current coding has created the situation above...access under a would be base structure, because you cannot close it off.