Hi,
There seems to be a deprecation affecting this bench command as shown below:
sudo -H bench setup lets-encrypt site1.local
Running this will stop the nginx service temporarily causing your sites to go offline
Do you want to continue? [y/N]: y
INFO:bench.utils:sudo systemctl stop nginx
INFO:bench.utils:/opt/certbot-auto --config /etc/letsencrypt/configs/site1.local.cfg certonly
Skipping bootstrap because certbot-auto is deprecated on this system.
Your system is not supported by certbot-auto anymore.
Certbot cannot be installed.
Please visit https://certbot.eff.org/ to check for other alternatives.
INFO:bench.utils:sudo systemctl start nginx
There was a problem trying to setup SSL for your site
A workaround is possible using manual approach of setting up letsencrypt, but perhaps a fix is needed in bench commands for letsencrypt. I would attempt the fix if I knew where to poke 
Ken