When assigning a tagged node to a site, the secondary parent isn't displayed (in the site filter)
1. Create a document under the repository (/Company Home/)
2. Add a tag to this document. (notice that the left bar has the "Tags filter" updated with the new tag)
3. Create a site.
4. Add this document to the site as a secondary parent with:
var document = search.findNode(<noderef from node created in step 1>);
5. Go to your sites document library
The tag filter in the sites document library should also have the tag in the tags filter.
The tag filter in the sites document library is empty.
The tag (collection) is set as a property on the node, the node now has two parents. Looking at the API, for the call findTagScope uses only the primary parent path:
"The 'nearest' tag scope is discovered by walking up the primary parent path until a tag scope is found or the root node is reached."