Yes, when first creating the certificate you can use
--cert-name to specify which name will be used in
/etc/letsencrypt to refer to that certificate.
Certbot obtains one new certificate each time you run it. So the idea would be to run Certbot one time per domain, if that's what you want, like
certbot certonly --nginx -d www.onedomain.com -d onedomain.com
certbot certonly --nginx -d www.anotherdomain.com -d anotherdomain.com
certbot certonly --nginx -d www.thirddomain.com -d thirddomain.com
If the names that you obtain certificates for are subdomains of the same domain, you might run into a rate limit (Certificates Per Registered Domain) by doing this.
If they are independent domains, this shouldn't be a problem at all.