I can choose which domain i want to added to the certificate, like mywebsite.com, mail.mywebsite.com, smtp.mywebsite.com
So i tried with and without smtp.mywebsite.com
If you configure the hostname in Joomla to smtp.mywebsite.com then you should have your certificate for mywebsite.com. This assumes the certificate is even properly setup for that domain name as I've no clue how your host is handling those.