I understand what you mean. My problem is that I need to create wildcard domain with easyengine as I do my projects in laravel (PHP) and this one project handles 5 domains.
So if you call www.example.com , sub.example.com and sub1.example.com I need to direct it to the same document root.
If I'll create subdomains with EE it will create separate document roots in /var/www for each of my subdomain so it'll create /var/www/sub.example.com and /var/www/sub1.example.com and what I need is to point all of them to /var/www/example.com and have Let's encrypt activated on all of them