Yes you are right- however what I was referring to is the choice of using an alias. My reasons being:
With the usage of calling the localdomain you'll get www, demo, test, or what ever you have as an alias, as in my case I have used store.mydomain.com, demo.mydomain.com, wholesale.mydomain.com , https://www.mydomain.com. etc. With an option to select what should actually be used in the mail options choices of what to enter as the domain would be a more convenient way to set it up.
I've seen many emails over time that when you try to reply to they bounce as they have an alias in the return, or they bounce from the start.
I really don't think I am the only one that had this problem, It took me over a month to actually find it and pin it down. The responses I was getting back from some of the mail server like Google gave no indication that this was the reason they weren't being accepted.
This is the response I was getting from google: deferral: 74.125.22.27_failed_after_I_sent_the_message./Remote_host_said:421-4.7.0[141.158.210.46##########_15]_Our_system_has_detected_an_unusual_rate_of/421-4.7.0_unsolicited_mail_originating_from_your_IP_address._To_protect_our/421-4.7.0_users_from_spam,_mail_sent_from_your_IP_address_has_been_temporarily/421-4.7.0_rate_limited._Please_visit/421-4.7.0_http://www.google.com/mail/help/bulk_mail.html_to_review_our_Bulk/421_4.7.0_Email_Senders_Guidelines._o1si7895348qcf.43_-_gsmtp/
And spending few days testing and reading trough the google guidelines there is not one mention of a malformed message id:
Someone without full admin access to their server isn't going to be able to track this down, or even know there is an issue. These messages are in the mail send logs only, they weren't showing up as bounces or anywhere a regular user is going to have access to on a hosted server.
And to make matters even more hard to track it down, is not all mail servers will reject the email due to this. I've only seen 5-6 that do, the rest accepted them.
Before switching to this much much better cart I used joomla/virtuemart with their stock phpmailer, If I recall correctly there was an option in that to set a domain name in the mailer? Phpmailer was the about the only thing that did work right with VM :-))
Anyway users having an issue with mail not going through you may also have them double check this also, as you do an excellent job helping and giving good advice.