Running this command will get you a new certificate that covers only
mail1.test.com. If you would like a certificate that covers both
mail.test.com, the command should be:
./letsencrypt-auto certonly --standalone -d mail.test.com -d mail1.test.com --expand
This would give you a SAN certificate covering both domains.
It’s also perfectly fine to have multiple certificates (with, for example, one domain each) on the same server. This would use SNI (Server Name Indication). One downside is that very old client or server software might not support SNI. Unless you have a specific reason why two certificates with SNI would be a better fit, SAN is probably your best option.