Hi,
Thank you for your kind words, and the details, it helps us a lot!
I believe you have two possible choices here:
1. To either change the logic, how the checkboxes are handled, right here: https://i.imgur.com/GP0QNia.png
2. and/or change this option: https://i.imgur.com/w5df3AL.png
I think I recommend both changes, it will prevent results showing up, which have no relation to the given taxonomy.