xxxxxxxxxx
When the user invokes certbot with -d, the Common Name field is set to the first domain passed via that argument .
Getting multiple names on a single cert is very easy.
With certbot:
Instead of the single: -d one.domain
Use:
-d one.domain -d two.domain -d three.domain …
or
-d 'one.domain,two.domain,three.domain,…'
[LE certs will hold 100 SAN entries]