I see what you mean.
Currently every term in every taxonomy is treated as one group so there is virtually no connection between the “Filter by Category” and the “Filter By Region” taxonomies. I'm rather not explain exactly why, but mostly because it has a great impact on the final search performance. Back when I did this part of the code, I had to rewrite it hundreds of times to come up with an optimal solution both on performance and usability, considering some users might have databases with over millions of records.
The good news is, that I have actually found a solution which I already implemented to the upcoming version. There is going to be an additional options, which allows you to set the logic between each taxonomy term group, as well as the term logic options is moved to the category & taxonomy panel for better comfort.
I'm making the final steps on the 4.7 release, which is going to be a huge update. Only testing remains, so I'm uploading it to codecanyon in 1-2 days, it should be available 24 hours after that.Best,
If you like my products, don't forget to rate them on codecanyon :)