LetsEncrypt for subdomains without www

I have a virtual server that is a subdomain. However, Virtualmin creates it with both sub.domain.com and www.sub.domain.com. I only have a dns entry for sub.domain.com. When I try to create a LetsEncrypt cert, it tries to verify with http://www.sub.domain.com/.well-know/etc...

I could not find a simple way in the code to modify this behavior. Nor could I find a way to remove the www alias from the subdomain. Because Virtualmin removed subdomains for sub servers, this www.sub.domain.com behavior happens and I am sure I'm not the first person to have this issue.

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Comments

On the form in Virtualmin where you request the Let's Encrypt cert, you should be able to enter the hostnames that it is requested for.