OK, let me be a bit more precise. The only way that certbot, running on the FreeNAS box, could automatically obtain a cert without significant manual configuration would be for the FreeNAS box to be directly exposed to the Internet--or at least for port 80 on the FreeNAS box to be directly exposed. There are plenty of ways that a user can obtain an LE cert for a FreeNAS box, but certbot running on the box itself isn't going to be a good one without additional manual, site-specific configuration. Best option is probably one of the alternate clients that supports the DNS challenge, like letsencrypt.sh or acme.sh, and a DNS provider that has an API you can use to automate updates to your DNS records.
One thing that would really help, though, would be an ability to add/change the TLS cert through the API.