Haven't tried this myself but... does this work if you fully qualify the grand-child hierarchy?

yml
    siteHierarchies:
        - root
        - parent
        - child
        - parent.child.grand-child  <-- perhaps you can also try omitting this one from siteHierarchies altogether?
    hierarchy:
        parent.child.grand-child:
            publishByDefault:
                public: false

@kevins8 in case he knows better