We need to be more precise in the help message for virtual navigation vocabularies, in the case of a hierarchical vocabulary.
For example something like:
"Provide vocabularies for the navigation tree. The first vocabulary will be used for the navigation tree roots, and the following ones are used for lower levels. In the case of a hierarchical vocabulary that holds both the root and child entries, you need to provide this vocabulary as many times as its number of levels, roots included. For example, for a 2-level vocabulary you would provide it twice: once for the tree roots, once for the lower level."