This is an interesting question, and I’m not sure yet on the best way to provide this functionality.
Spatial structure breakdown is a fundamental part of IFC, with a one to many children relationship that matches rhino layer hierarchy so that works nicely for this. Ie a spatial element only has one parent or host. Zones are a “group” of spaces, and a space can relate to multiple zones.
Do you model each space as a layer or as rhino objects representing envelope? We could perhaps have specific tree nodes for zones and allow drag and drop (with right context delete).
The other option is to set zones up as a template (similar to your building storey question) and merge that or store it in the rhino document.