Lets Encrypt certificate with a Virtualmin subserver results in Security error/Deceptive site ahead

I am veering off-topic so I will be brief:

  1. Your search engine rankings could be impacted @ferd-z if you have random subdomains under the domain of your primary brand.

  2. If you must use subdomains for staging customer websites, then do this: create virtual server for your client domain even if it not yet registered or configured to work with your server and then create an alias for that virtual server and use your subdomain as an alias.

Use the alias for staging the website and when the customer has pointed his domain to your server, delete the alias.

E.g.
https://sheherwali.indiax.com was the staging domain (alias)
https://sheherwali.co.in is the customer domain

If you wish to discuss this further, please start a new topic.