Created attachment 193459 [details] replaces nginx root folder Certbot Nginx plugin hardcodes nginx root to /etc/nginx. Patch rewrites it to /usr/local/etc/nginx Ideally this should be a config entry. I'd check if you can land such a patch upstream.
Created attachment 193460 [details] replaces-nginx-rootfolder
Looking closely nginx plugin exposes --server-root to change nginx root, but IMO its better to replace the default on FreeBSD systems.
A commit references this bug: Author: sunpoet Date: Thu May 17 18:30:55 UTC 2018 New revision: 470243 URL: https://svnweb.freebsd.org/changeset/ports/470243 Log: Fix nginx server root path - Bump PORTREVISION for package change PR: 228294 Reported by: Dhananjay Balan <mail@dbalan.in> Changes: head/security/py-certbot-nginx/Makefile
Committed. Thanks!