I'm confused. When I create a new User and Email, some domains show host.domain.com, others show host.domain.com and domain.com I only want to use domain.com but I'm unable to select this.
You are able to select this in 2.3.3. Have a look at the checkboxes in the email settings of the mail account, there is a checkbox for every domain assigned to this website.
After the upgrade there was no checkbox. I had to delete the whole domain and start all over again. Then indeed there's a checkbox.