Just an idea how you could create SSL certificates using Let’s Encrypt for your clients mail domains in ISPConfig and have it being delivered via Postfix and Dovecot to prevent certificate warnings in email clients. But this method has it’s downside.
How to install ISPConfig 3.1 on Ubuntu 16.04 on a Digital Ocean Server incl. Apache as web server, Postfix as mail server, Pure FTPD as file server, Let’s Encrypt for real SSL Certificates, MariaDB as database server, fail2ban to limit login attempts, and very much more.
Using a real SMPT mail box will help a lot to have your WooCommerce E-Mails send to the customers INBOX instead of spam. To get this done, any WordPress installation I am in charge with, get it’s own Mail Account. Also make sure your DNS settings are setup correctly to make sure your mails are not being treated as SPAM.