hey, what a good project.

However setup-ngxblocker doesn't detect the 301 Redirects most people use, and simply adds:

include /etc/nginx/bots.d/ddos.conf; include /etc/nginx/bots.d/blockbots.conf; 

in the last server block found. This just cannot work.
Following best practices (if any?), the last server blocks of a vhost should be used for redirects.

Thus, it would make more sense to your setup-ngxblocker script to add these includes in the server blockS that contain a root directive only. Wouldn't it?