I'm also a bit confused about groups and "non-shape-based" objects having shapes...
There was something rather clear before, that anything derived from Part::Feature has a Shape, others not (or at least, it's not assumed that they have one)
All "containers" Arch objects (Project, Site, BuildingPart) are actually simple "shapeless" objects with a Group extension, not like App::Parts. The BuildingPart also holds a Shape property that is only for internal use, not meant to be displayed.
However, BuildingParts are behaving correctly, but Projects and Sites not. Maybe adding an empty, dummy "Shape" property to them would solve the issue? I'll do some testing