Thanks for your plugin. I'm currently testing it out, hoping to replace the Query Multiple Taxonomies I'm using now.
It seems that the plugin can't recognize shared taxonomies.
For example, I have the taxonomy "metro" registered under "teacher" and "school" CPTs.
I create a search form to only include "teacher" CPT and hide empty taxonomies. For simple testing purposes, I only have one post for "teacher" which has a "metro" term "Alegre" and one post for "class" which has a "metro" term "Triste". However, when the search form is generated, it shows both "Alegre" and "Triste" when there should only appear "Alegre".
Naturally, if someone selects "Triste" as a term to search, then they are sent to a Not Found page.