some months ago you had to install letsencrypt manually on new systems, but now it seems that its installed by default, which gives me a headache.
when creating a new host i like to automatically have a self singed cert created instead of letsencrypt (self-signed will later be replaced by a real cert).
You could reconfigure Virtualmin to keep SSL for websites disabled at the time of creating virtual servers via Virtualmin -> System Settings -> Server Templates.
When you later wish to apply a SSL certificate from an authority other than Let’s Encrypt, just Virtualmin -> Edit Virtual Server and check the box for SSL certificate for website. Then go on to apply the certificate as usual.