What I’ll do for the next release is allow the default directs (which can be setup on the Server Templates page under Website for domain) to include the hostname, so you can create a direct from mail.${DOM} to www.${DOM} for all new servers.
Yes that is correct. Or for existing domains, you could set it up on the Website Redirects page.
Obviously there are a couple of method that we as admins can do manually to fix/patch this, however I am more into automated solutions or semi-automated in the case of pre-exisiting sites where the user needs to stop and start something. Witht he second option this will be done over time because not all admin will know about this or want to do it.
I appreciate this is not a world ending issue 
However, it could be serious for those using Apache and their clients who are concerned about their SEO positioning.
It is not a mailto link that does it. Google reads the SSL certificate and gets the Alternative Names`, my feelings is that this will happen on nginx systems .
Also my quantumwarp.com has a lot of content and is the one indexed, whereas I have a couple of other sites and their mail.domain.com has not been indexed.
But I have not found this (I searched a couple of other sites that have pretty good SEO ratings and they are all OK - all on Nginx (obviously have no .htaccess) all with current LE Certs most also have active mail in/out (mostly using Roundcube but not all) all set up to point www.to domain.com - just using the standard Website Configuration->Website Options to redirect to SSL.
hence - my disbelief! (I would obviously like to stop worrying about this - unless it can be confirmed that it also affects Nginx sites)
if in a browser you can see a website on mail.domain.com google does not care if your are running nginx or apache or caddy and might index it.
Try browsing these websites for 5 minutes with Google Chrome browser and see if that kicks things off.
Also I would not worry about this as @Jamie is looking at a solution and as @calport says you can use cannonical tags or as you suggest redirect commands.
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I assume they also are similar (built with Virtualmin, have valid Certs, are Apache, .etc. ) then what is the difference - obviously there is inconsistency here. Perhaps it would be better to find out why - before implementing a solution?
FYI, the next release of Virtualmin will make it easier to redirect all sub-domains of yourdomain.com (like mail, ftp, etc) to yourdomain.com to avoid this kind of issue.
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In the upcoming version. Of virtualmin Jamie has added an option to fix this.
Lol, he said this above and my post was not needed.
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