Certbot reads Nginx config from /etc/nginx/ by default.

It won't work when Nginx has a different config path.

nginx -c can make it work but fails after an Nginx restart.

In addition to an Nginx binary rebuild with --conf-path=/etc/nginx/nginx.conf

Here comes the trick......

$ mkdir /etc/nginx
$ cp /usr/local/nginx/conf/* /etc/nginx/
$ mv /usr/local/nginx/conf /usr/local/nginx/conf_bak

# Make a symbolic link to your Nginx config path
$ ln -s /etc/nginx/ /usr/local/nginx/conf